From bb022462de55ca38d3c6aa46232741edde52716f Mon Sep 17 00:00:00 2001
From: igordot <6363505+igordot@users.noreply.github.com>
Date: Sat, 21 Dec 2024 04:50:22 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20igordot/?=
 =?UTF-8?q?msigdbr@32130ead882554e163160455c2090fa29c31c476=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                            |  2 +-
 LICENSE-text.html                   |  2 +-
 LICENSE.html                        |  2 +-
 articles/index.html                 |  2 +-
 articles/msigdbr-intro.html         | 44 ++++++++++++++---------------
 authors.html                        |  6 ++--
 index.html                          |  2 +-
 news/index.html                     |  9 ++++--
 pkgdown.yml                         |  2 +-
 reference/index.html                |  2 +-
 reference/msigdbr.html              | 30 ++++++++++----------
 reference/msigdbr_collections.html  | 12 ++++----
 reference/msigdbr_show_species.html |  2 +-
 reference/msigdbr_species.html      |  2 +-
 reference/pipe.html                 |  2 +-
 search.json                         |  2 +-
 16 files changed, 64 insertions(+), 59 deletions(-)

diff --git a/404.html b/404.html
index 9e85b11..791b1ef 100644
--- a/404.html
+++ b/404.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="https://igordot.github.io/msigdbr/index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 25d2040..3dbd06b 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 8d32011..3856d8d 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index a644af3..5e20f41 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/msigdbr-intro.html b/articles/msigdbr-intro.html
index 201fdae..b37ce26 100644
--- a/articles/msigdbr-intro.html
+++ b/articles/msigdbr-intro.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -104,12 +104,12 @@ <h2 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 6 × 18</span></span></span>
 <span><span class="co">#&gt;   gs_cat gs_subcat     gs_name gene_symbol entrez_gene ensembl_gene human_gene…¹</span></span>
 <span><span class="co">#&gt;   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>             <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> C3     MIR:MIR_Lega… AAACCA… Abcc4            <span style="text-decoration: underline;">239</span>273 ENSMUSG0000… ABCC4       </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> C3     MIR:MIR_Lega… AAACCA… Abraxas2         <span style="text-decoration: underline;">109</span>359 ENSMUSG0000… ABRAXAS2    </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C3     MIR:MIR_Lega… AAACCA… Actn4             <span style="text-decoration: underline;">60</span>595 ENSMUSG0000… ACTN4       </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> C3     MIR:MIR_Lega… AAACCA… Acvr1             <span style="text-decoration: underline;">11</span>477 ENSMUSG0000… ACVR1       </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> C3     MIR:MIR_Lega… AAACCA… Adam9             <span style="text-decoration: underline;">11</span>502 ENSMUSG0000… ADAM9       </span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">6</span> C3     MIR:MIR_Lega… AAACCA… Adamts5           <span style="text-decoration: underline;">23</span>794 ENSMUSG0000… ADAMTS5     </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> C3     MIR:MIR_LEGA… AAACCA… Abcc4            <span style="text-decoration: underline;">239</span>273 ENSMUSG0000… ABCC4       </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> C3     MIR:MIR_LEGA… AAACCA… Abraxas2         <span style="text-decoration: underline;">109</span>359 ENSMUSG0000… ABRAXAS2    </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> C3     MIR:MIR_LEGA… AAACCA… Actn4             <span style="text-decoration: underline;">60</span>595 ENSMUSG0000… ACTN4       </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> C3     MIR:MIR_LEGA… AAACCA… Acvr1             <span style="text-decoration: underline;">11</span>477 ENSMUSG0000… ACVR1       </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">5</span> C3     MIR:MIR_LEGA… AAACCA… Adam9             <span style="text-decoration: underline;">11</span>502 ENSMUSG0000… ADAM9       </span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">6</span> C3     MIR:MIR_LEGA… AAACCA… Adamts5           <span style="text-decoration: underline;">23</span>794 ENSMUSG0000… ADAMTS5     </span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ abbreviated name: ¹​human_gene_symbol</span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 11 more variables: human_entrez_gene &lt;int&gt;, human_ensembl_gene &lt;chr&gt;,</span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;">#   gs_id &lt;chr&gt;, gs_pmid &lt;chr&gt;, gs_geoid &lt;chr&gt;, gs_exact_source &lt;chr&gt;,</span></span></span>
@@ -217,28 +217,28 @@ <h2 id="helper-functions">Helper functions<a class="anchor" aria-label="anchor"
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 23 × 3</span></span></span>
 <span><span class="co">#&gt;    gs_cat gs_subcat         num_genesets</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                    <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> C1     <span style="color: #949494;">""</span>                         299</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> C2     <span style="color: #949494;">"</span>CGP<span style="color: #949494;">"</span>                     <span style="text-decoration: underline;">3</span>399</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> C1     <span style="color: #949494;">""</span>                         300</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> C2     <span style="color: #949494;">"</span>CGP<span style="color: #949494;">"</span>                     <span style="text-decoration: underline;">3</span>405</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> C2     <span style="color: #949494;">"</span>CP<span style="color: #949494;">"</span>                        29</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> C2     <span style="color: #949494;">"</span>CP:BIOCARTA<span style="color: #949494;">"</span>              292</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> C2     <span style="color: #949494;">"</span>CP:KEGG<span style="color: #949494;">"</span>                  186</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> C2     <span style="color: #949494;">"</span>CP:PID<span style="color: #949494;">"</span>                   196</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> C2     <span style="color: #949494;">"</span>CP:REACTOME<span style="color: #949494;">"</span>             <span style="text-decoration: underline;">1</span>635</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> C2     <span style="color: #949494;">"</span>CP:WIKIPATHWAYS<span style="color: #949494;">"</span>          712</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> C2     <span style="color: #949494;">"</span>CP:REACTOME<span style="color: #949494;">"</span>             <span style="text-decoration: underline;">1</span>654</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> C2     <span style="color: #949494;">"</span>CP:WIKIPATHWAYS<span style="color: #949494;">"</span>          733</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> C3     <span style="color: #949494;">"</span>MIR:MIRDB<span style="color: #949494;">"</span>               <span style="text-decoration: underline;">2</span>377</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> C3     <span style="color: #949494;">"</span>MIR:MIR_Legacy<span style="color: #949494;">"</span>           221</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">11</span> C3     <span style="color: #949494;">"</span>TFT:GTRD<span style="color: #949494;">"</span>                 517</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">12</span> C3     <span style="color: #949494;">"</span>TFT:TFT_Legacy<span style="color: #949494;">"</span>           610</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> C3     <span style="color: #949494;">"</span>MIR:MIR_LEGACY<span style="color: #949494;">"</span>           221</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">11</span> C3     <span style="color: #949494;">"</span>TFT:GTRD<span style="color: #949494;">"</span>                 505</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">12</span> C3     <span style="color: #949494;">"</span>TFT:TFT_LEGACY<span style="color: #949494;">"</span>           610</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">13</span> C4     <span style="color: #949494;">"</span>CGN<span style="color: #949494;">"</span>                      427</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">14</span> C4     <span style="color: #949494;">"</span>CM<span style="color: #949494;">"</span>                       431</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">15</span> C5     <span style="color: #949494;">"</span>GO:BP<span style="color: #949494;">"</span>                   <span style="text-decoration: underline;">7</span>763</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">16</span> C5     <span style="color: #949494;">"</span>GO:CC<span style="color: #949494;">"</span>                   <span style="text-decoration: underline;">1</span>035</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">17</span> C5     <span style="color: #949494;">"</span>GO:MF<span style="color: #949494;">"</span>                   <span style="text-decoration: underline;">1</span>763</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">18</span> C5     <span style="color: #949494;">"</span>HPO<span style="color: #949494;">"</span>                     <span style="text-decoration: underline;">5</span>142</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">15</span> C5     <span style="color: #949494;">"</span>GO:BP<span style="color: #949494;">"</span>                   <span style="text-decoration: underline;">7</span>751</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">16</span> C5     <span style="color: #949494;">"</span>GO:CC<span style="color: #949494;">"</span>                   <span style="text-decoration: underline;">1</span>009</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">17</span> C5     <span style="color: #949494;">"</span>GO:MF<span style="color: #949494;">"</span>                   <span style="text-decoration: underline;">1</span>772</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">18</span> C5     <span style="color: #949494;">"</span>HPO<span style="color: #949494;">"</span>                     <span style="text-decoration: underline;">5</span>405</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">19</span> C6     <span style="color: #949494;">""</span>                         189</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">20</span> C7     <span style="color: #949494;">"</span>IMMUNESIGDB<span style="color: #949494;">"</span>             <span style="text-decoration: underline;">4</span>872</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">21</span> C7     <span style="color: #949494;">"</span>VAX<span style="color: #949494;">"</span>                      347</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">22</span> C8     <span style="color: #949494;">""</span>                         704</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">22</span> C8     <span style="color: #949494;">""</span>                         830</span></span>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">23</span> H      <span style="color: #949494;">""</span>                          50</span></span></code></pre></div>
 </div>
 <div class="section level2">
@@ -273,9 +273,9 @@ <h2 id="pathway-enrichment-analysis">Pathway enrichment analysis<a class="anchor
 <h2 id="potential-questions-or-concerns">Potential questions or concerns<a class="anchor" aria-label="anchor" href="#potential-questions-or-concerns"></a>
 </h2>
 <p><strong>Which version of MSigDB was used?</strong></p>
-<p>This package was generated with MSigDB v2022.1. The MSigDB version is
-used as the base of the msigdbr CRAN package version. You can check the
-installed version with <code>packageVersion("msigdbr")</code>.</p>
+<p>This package was generated with MSigDB v2023.1.Hs. The MSigDB version
+is used as the base of the msigdbr CRAN package version. You can check
+the installed version with <code>packageVersion("msigdbr")</code>.</p>
 <p><strong>Can I download the gene sets directly from MSigDB instead of
 using this package?</strong></p>
 <p>Yes. You can then import the GMT files (with <code>getGmt()</code>
diff --git a/authors.html b/authors.html
index 9b6d34a..5245432 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -45,13 +45,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Dolgalev I (2024).
 <em>msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format</em>.
-R package version 2022.1.1, <a href="https://igordot.github.io/msigdbr/">https://igordot.github.io/msigdbr/</a>.
+R package version 2023.1.1, <a href="https://igordot.github.io/msigdbr/">https://igordot.github.io/msigdbr/</a>.
 </p>
       <pre>@Manual{,
   title = {msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format},
   author = {Igor Dolgalev},
   year = {2024},
-  note = {R package version 2022.1.1},
+  note = {R package version 2023.1.1},
   url = {https://igordot.github.io/msigdbr/},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 74adeae..b8fb4b2 100644
--- a/index.html
+++ b/index.html
@@ -25,7 +25,7 @@
 
     <a class="navbar-brand me-2" href="index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index a09dc85..bc1f746 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,9 +31,14 @@ <h1>Changelog</h1>
       <small>Source: <a href="https://github.com/igordot/msigdbr/blob/main/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="2023.1.1" id="msigdbr-202311">msigdbr 2023.1.1<a class="anchor" aria-label="anchor" href="#msigdbr-202311"></a></h2>
+<ul><li>Based on MSigDB v2023.1.Hs release.</li>
+<li>Not on CRAN.</li>
+</ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="2022.1.1" id="msigdbr-202211">msigdbr 2022.1.1<a class="anchor" aria-label="anchor" href="#msigdbr-202211"></a></h2>
-<ul><li>Based on MSigDB v2022.1 release.</li>
+<ul><li>Based on MSigDB v2022.1.Hs release.</li>
 <li>Not on CRAN.</li>
 </ul></div>
     <div class="section level2">
diff --git a/pkgdown.yml b/pkgdown.yml
index 158e9af..c49dd7c 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   msigdbr-intro: msigdbr-intro.html
-last_built: 2024-12-21T04:45Z
+last_built: 2024-12-21T04:50Z
 urls:
   reference: https://igordot.github.io/msigdbr/reference
   article: https://igordot.github.io/msigdbr/articles
diff --git a/reference/index.html b/reference/index.html
index 2cbf39a..b599907 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/msigdbr.html b/reference/msigdbr.html
index 82b485e..df093fa 100644
--- a/reference/msigdbr.html
+++ b/reference/msigdbr.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -74,20 +74,20 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># get all human gene sets</span></span></span>
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="fu">msigdbr</span><span class="op">(</span>species <span class="op">=</span> <span class="st">"Homo sapiens"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3,995,746 × 15</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4,029,754 × 15</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    gs_cat gs_subcat      gs_name        gene_symbol entrez_gene ensembl_gene   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>             <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 ABCC4             <span style="text-decoration: underline;">10</span>257 ENSG00000125257</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 ABRAXAS2          <span style="text-decoration: underline;">23</span>172 ENSG00000165660</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 ACTN4                81 ENSG00000130402</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 ACVR1                90 ENSG00000115170</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 ADAM9              <span style="text-decoration: underline;">8</span>754 ENSG00000168615</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 ADAMTS5           <span style="text-decoration: underline;">11</span>096 ENSG00000154736</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 AMER2            <span style="text-decoration: underline;">219</span>287 ENSG00000165566</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 ANK2                287 ENSG00000145362</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 API5               <span style="text-decoration: underline;">8</span>539 ENSG00000166181</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C3     MIR:MIR_Legacy AAACCAC_MIR140 BACH1               571 ENSG00000156273</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 3,995,736 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 ABCC4             <span style="text-decoration: underline;">10</span>257 ENSG00000125257</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 ABRAXAS2          <span style="text-decoration: underline;">23</span>172 ENSG00000165660</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 ACTN4                81 ENSG00000130402</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 ACVR1                90 ENSG00000115170</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 ADAM9              <span style="text-decoration: underline;">8</span>754 ENSG00000168615</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 ADAMTS5           <span style="text-decoration: underline;">11</span>096 ENSG00000154736</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 AMER2            <span style="text-decoration: underline;">219</span>287 ENSG00000165566</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 ANK2                287 ENSG00000145362</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 API5               <span style="text-decoration: underline;">8</span>539 ENSG00000166181</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C3     MIR:MIR_LEGACY AAACCAC_MIR140 ATOSA             <span style="text-decoration: underline;">56</span>204 ENSG00000047346</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,029,744 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: human_gene_symbol &lt;chr&gt;, human_entrez_gene &lt;int&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   human_ensembl_gene &lt;chr&gt;, gs_id &lt;chr&gt;, gs_pmid &lt;chr&gt;, gs_geoid &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   gs_exact_source &lt;chr&gt;, gs_url &lt;chr&gt;, gs_description &lt;chr&gt;</span></span>
@@ -96,7 +96,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co"># get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets</span></span></span>
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="fu">msigdbr</span><span class="op">(</span>species <span class="op">=</span> <span class="st">"Mus musculus"</span>, category <span class="op">=</span> <span class="st">"C2"</span>, subcategory <span class="op">=</span> <span class="st">"CGP"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 378,755 × 18</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 378,935 × 18</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    gs_cat gs_subcat gs_name                 gene_symbol entrez_gene ensembl_gene</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>             <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> C2     CGP       ABBUD_LIF_SIGNALING_1_… Ahnak             <span style="text-decoration: underline;">66</span>395 ENSMUSG0000…</span>
@@ -109,7 +109,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> C2     CGP       ABBUD_LIF_SIGNALING_1_… Cd24a             <span style="text-decoration: underline;">12</span>484 ENSMUSG0000…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C2     CGP       ABBUD_LIF_SIGNALING_1_… Cyfip1            <span style="text-decoration: underline;">20</span>430 ENSMUSG0000…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C2     CGP       ABBUD_LIF_SIGNALING_1_… Dcaf11            <span style="text-decoration: underline;">28</span>199 ENSMUSG0000…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 378,745 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 378,925 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 12 more variables: human_gene_symbol &lt;chr&gt;, human_entrez_gene &lt;int&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   human_ensembl_gene &lt;chr&gt;, gs_id &lt;chr&gt;, gs_pmid &lt;chr&gt;, gs_geoid &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   gs_exact_source &lt;chr&gt;, gs_url &lt;chr&gt;, gs_description &lt;chr&gt;, taxon_id &lt;int&gt;,</span></span>
diff --git a/reference/msigdbr_collections.html b/reference/msigdbr_collections.html
index 839f43b..f88502d 100644
--- a/reference/msigdbr_collections.html
+++ b/reference/msigdbr_collections.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -52,16 +52,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 23 × 3</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    gs_cat gs_subcat         num_genesets</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>                    <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> C1     <span style="color: #949494;">""</span>                         299</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C2     <span style="color: #949494;">"</span>CGP<span style="color: #949494;">"</span>                     <span style="text-decoration: underline;">3</span>399</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> C1     <span style="color: #949494;">""</span>                         300</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> C2     <span style="color: #949494;">"</span>CGP<span style="color: #949494;">"</span>                     <span style="text-decoration: underline;">3</span>405</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C2     <span style="color: #949494;">"</span>CP<span style="color: #949494;">"</span>                        29</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> C2     <span style="color: #949494;">"</span>CP:BIOCARTA<span style="color: #949494;">"</span>              292</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> C2     <span style="color: #949494;">"</span>CP:KEGG<span style="color: #949494;">"</span>                  186</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> C2     <span style="color: #949494;">"</span>CP:PID<span style="color: #949494;">"</span>                   196</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C2     <span style="color: #949494;">"</span>CP:REACTOME<span style="color: #949494;">"</span>             <span style="text-decoration: underline;">1</span>635</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> C2     <span style="color: #949494;">"</span>CP:WIKIPATHWAYS<span style="color: #949494;">"</span>          712</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C2     <span style="color: #949494;">"</span>CP:REACTOME<span style="color: #949494;">"</span>             <span style="text-decoration: underline;">1</span>654</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> C2     <span style="color: #949494;">"</span>CP:WIKIPATHWAYS<span style="color: #949494;">"</span>          733</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C3     <span style="color: #949494;">"</span>MIR:MIRDB<span style="color: #949494;">"</span>               <span style="text-decoration: underline;">2</span>377</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C3     <span style="color: #949494;">"</span>MIR:MIR_Legacy<span style="color: #949494;">"</span>           221</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C3     <span style="color: #949494;">"</span>MIR:MIR_LEGACY<span style="color: #949494;">"</span>           221</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 13 more rows</span></span>
 </code></pre></div>
     </div>
diff --git a/reference/msigdbr_show_species.html b/reference/msigdbr_show_species.html
index 626c1d0..612d6b2 100644
--- a/reference/msigdbr_show_species.html
+++ b/reference/msigdbr_show_species.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/msigdbr_species.html b/reference/msigdbr_species.html
index cd82676..ecddc50 100644
--- a/reference/msigdbr_species.html
+++ b/reference/msigdbr_species.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/pipe.html b/reference/pipe.html
index 91e187f..4e9b746 100644
--- a/reference/pipe.html
+++ b/reference/pipe.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">msigdbr</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2022.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2023.1.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 3ec23fc..8353bf2 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to msigdbr","text":"Pathway analysis common task genomics research many available R-based software tools. Depending tool, may necessary import pathways, translate genes appropriate species, convert symbols IDs, format resulting object. msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets typically used Gene Set Enrichment Analysis (GSEA) software: R-friendly “tidy” format one gene pair per row multiple frequently studied model organisms, mouse, rat, pig, zebrafish, fly, yeast, addition original human genes gene symbols well NCBI Entrez Ensembl IDs without accessing external resources requiring active internet connection Please aware homologs computationally predicted distinct genes. full pathways may well conserved across species.","code":""},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to msigdbr","text":"package can installed CRAN.","code":"install.packages(\"msigdbr\")"},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"usage","dir":"Articles","previous_headings":"","what":"Usage","title":"Introduction to msigdbr","text":"Load package. gene sets database can retrieved specifying species interest. can retrieve data just specific collection/category, hallmark gene sets. can specify sub-category, C2 (curated) CGP (chemical genetic perturbations) gene sets. require custom filtering, msigdbr() function output data frame can manipulated using standard methods. example, can subset specific collection/category using dplyr::filter().","code":"library(msigdbr) #> Error in get(paste0(generic, \".\", class), envir = get_method_env()) :  #>   object 'type_sum.accel' not found all_gene_sets <- msigdbr(species = \"Mus musculus\") head(all_gene_sets) #> # A tibble: 6 × 18 #>   gs_cat gs_subcat     gs_name gene_symbol entrez_gene ensembl_gene human_gene…¹ #>   <chr>  <chr>         <chr>   <chr>             <int> <chr>        <chr>        #> 1 C3     MIR:MIR_Lega… AAACCA… Abcc4            239273 ENSMUSG0000… ABCC4        #> 2 C3     MIR:MIR_Lega… AAACCA… Abraxas2         109359 ENSMUSG0000… ABRAXAS2     #> 3 C3     MIR:MIR_Lega… AAACCA… Actn4             60595 ENSMUSG0000… ACTN4        #> 4 C3     MIR:MIR_Lega… AAACCA… Acvr1             11477 ENSMUSG0000… ACVR1        #> 5 C3     MIR:MIR_Lega… AAACCA… Adam9             11502 ENSMUSG0000… ADAM9        #> 6 C3     MIR:MIR_Lega… AAACCA… Adamts5           23794 ENSMUSG0000… ADAMTS5      #> # ℹ abbreviated name: ¹​human_gene_symbol #> # ℹ 11 more variables: human_entrez_gene <int>, human_ensembl_gene <chr>, #> #   gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, gs_exact_source <chr>, #> #   gs_url <chr>, gs_description <chr>, taxon_id <int>, ortholog_sources <chr>, #> #   num_ortholog_sources <dbl> h_gene_sets <- msigdbr(species = \"mouse\", category = \"H\") head(h_gene_sets) #> # A tibble: 6 × 18 #>   gs_cat gs_subcat gs_name     gene_symbol entrez_gene ensembl_gene human_gene…¹ #>   <chr>  <chr>     <chr>       <chr>             <int> <chr>        <chr>        #> 1 H      \"\"        HALLMARK_A… Abca1             11303 ENSMUSG0000… ABCA1        #> 2 H      \"\"        HALLMARK_A… Abcb8             74610 ENSMUSG0000… ABCB8        #> 3 H      \"\"        HALLMARK_A… Acaa2             52538 ENSMUSG0000… ACAA2        #> 4 H      \"\"        HALLMARK_A… Acadl             11363 ENSMUSG0000… ACADL        #> 5 H      \"\"        HALLMARK_A… Acadm             11364 ENSMUSG0000… ACADM        #> 6 H      \"\"        HALLMARK_A… Acads             11409 ENSMUSG0000… ACADS        #> # ℹ abbreviated name: ¹​human_gene_symbol #> # ℹ 11 more variables: human_entrez_gene <int>, human_ensembl_gene <chr>, #> #   gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, gs_exact_source <chr>, #> #   gs_url <chr>, gs_description <chr>, taxon_id <int>, ortholog_sources <chr>, #> #   num_ortholog_sources <dbl> cgp_gene_sets <- msigdbr(species = \"mouse\", category = \"C2\", subcategory = \"CGP\") head(cgp_gene_sets) #> # A tibble: 6 × 18 #>   gs_cat gs_subcat gs_name     gene_symbol entrez_gene ensembl_gene human_gene…¹ #>   <chr>  <chr>     <chr>       <chr>             <int> <chr>        <chr>        #> 1 C2     CGP       ABBUD_LIF_… Ahnak             66395 ENSMUSG0000… AHNAK        #> 2 C2     CGP       ABBUD_LIF_… Alcam             11658 ENSMUSG0000… ALCAM        #> 3 C2     CGP       ABBUD_LIF_… Ankrd40           71452 ENSMUSG0000… ANKRD40      #> 4 C2     CGP       ABBUD_LIF_… Arid1a            93760 ENSMUSG0000… ARID1A       #> 5 C2     CGP       ABBUD_LIF_… Bckdhb            12040 ENSMUSG0000… BCKDHB       #> 6 C2     CGP       ABBUD_LIF_… AU021092         239691 ENSMUSG0000… C16orf89     #> # ℹ abbreviated name: ¹​human_gene_symbol #> # ℹ 11 more variables: human_entrez_gene <int>, human_ensembl_gene <chr>, #> #   gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, gs_exact_source <chr>, #> #   gs_url <chr>, gs_description <chr>, taxon_id <int>, ortholog_sources <chr>, #> #   num_ortholog_sources <dbl> all_gene_sets %>%   dplyr::filter(gs_cat == \"H\") %>%   head() #> # A tibble: 6 × 18 #>   gs_cat gs_subcat gs_name     gene_symbol entrez_gene ensembl_gene human_gene…¹ #>   <chr>  <chr>     <chr>       <chr>             <int> <chr>        <chr>        #> 1 H      \"\"        HALLMARK_A… Abca1             11303 ENSMUSG0000… ABCA1        #> 2 H      \"\"        HALLMARK_A… Abcb8             74610 ENSMUSG0000… ABCB8        #> 3 H      \"\"        HALLMARK_A… Acaa2             52538 ENSMUSG0000… ACAA2        #> 4 H      \"\"        HALLMARK_A… Acadl             11363 ENSMUSG0000… ACADL        #> 5 H      \"\"        HALLMARK_A… Acadm             11364 ENSMUSG0000… ACADM        #> 6 H      \"\"        HALLMARK_A… Acads             11409 ENSMUSG0000… ACADS        #> # ℹ abbreviated name: ¹​human_gene_symbol #> # ℹ 11 more variables: human_entrez_gene <int>, human_ensembl_gene <chr>, #> #   gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, gs_exact_source <chr>, #> #   gs_url <chr>, gs_description <chr>, taxon_id <int>, ortholog_sources <chr>, #> #   num_ortholog_sources <dbl>"},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"helper-functions","dir":"Articles","previous_headings":"","what":"Helper functions","title":"Introduction to msigdbr","text":"msigdbr_species() msigdbr_collections() helper functions assist setting msigdbr() parameters. can check available species msigdbr_species(). Either scientific common names acceptable msigdbr() function. can check available collections msigdbr_collections().","code":"msigdbr_species() #> # A tibble: 20 × 2 #>    species_name                    species_common_name                           #>    <chr>                           <chr>                                         #>  1 Anolis carolinensis             Carolina anole, green anole                   #>  2 Bos taurus                      bovine, cattle, cow, dairy cow, domestic cat… #>  3 Caenorhabditis elegans          NA                                            #>  4 Canis lupus familiaris          dog, dogs                                     #>  5 Danio rerio                     leopard danio, zebra danio, zebra fish, zebr… #>  6 Drosophila melanogaster         fruit fly                                     #>  7 Equus caballus                  domestic horse, equine, horse                 #>  8 Felis catus                     cat, cats, domestic cat                       #>  9 Gallus gallus                   bantam, chicken, chickens, Gallus domesticus  #> 10 Homo sapiens                    human                                         #> 11 Macaca mulatta                  rhesus macaque, rhesus macaques, Rhesus monk… #> 12 Monodelphis domestica           gray short-tailed opossum                     #> 13 Mus musculus                    house mouse, mouse                            #> 14 Ornithorhynchus anatinus        duck-billed platypus, duckbill platypus, pla… #> 15 Pan troglodytes                 chimpanzee                                    #> 16 Rattus norvegicus               brown rat, Norway rat, rat, rats              #> 17 Saccharomyces cerevisiae        baker's yeast, brewer's yeast, S. cerevisiae  #> 18 Schizosaccharomyces pombe 972h- NA                                            #> 19 Sus scrofa                      pig, pigs, swine, wild boar                   #> 20 Xenopus tropicalis              tropical clawed frog, western clawed frog msigdbr_collections() #> # A tibble: 23 × 3 #>    gs_cat gs_subcat         num_genesets #>    <chr>  <chr>                    <int> #>  1 C1     \"\"                         299 #>  2 C2     \"CGP\"                     3399 #>  3 C2     \"CP\"                        29 #>  4 C2     \"CP:BIOCARTA\"              292 #>  5 C2     \"CP:KEGG\"                  186 #>  6 C2     \"CP:PID\"                   196 #>  7 C2     \"CP:REACTOME\"             1635 #>  8 C2     \"CP:WIKIPATHWAYS\"          712 #>  9 C3     \"MIR:MIRDB\"               2377 #> 10 C3     \"MIR:MIR_Legacy\"           221 #> 11 C3     \"TFT:GTRD\"                 517 #> 12 C3     \"TFT:TFT_Legacy\"           610 #> 13 C4     \"CGN\"                      427 #> 14 C4     \"CM\"                       431 #> 15 C5     \"GO:BP\"                   7763 #> 16 C5     \"GO:CC\"                   1035 #> 17 C5     \"GO:MF\"                   1763 #> 18 C5     \"HPO\"                     5142 #> 19 C6     \"\"                         189 #> 20 C7     \"IMMUNESIGDB\"             4872 #> 21 C7     \"VAX\"                      347 #> 22 C8     \"\"                         704 #> 23 H      \"\"                          50"},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"pathway-enrichment-analysis","dir":"Articles","previous_headings":"","what":"Pathway enrichment analysis","title":"Introduction to msigdbr","text":"msigdbr output can used various pathway analysis packages. Use gene sets data frame clusterProfiler genes Entrez Gene IDs. Use gene sets data frame clusterProfiler genes gene symbols. Use gene sets data frame fgsea. Use gene sets data frame GSVA.","code":"msigdbr_t2g <- msigdbr_df %>%   dplyr::distinct(gs_name, entrez_gene) %>%   as.data.frame() enricher(gene = gene_ids_vector, TERM2GENE = msigdbr_t2g, ...) msigdbr_t2g <- msigdbr_df %>%   dplyr::distinct(gs_name, gene_symbol) %>%   as.data.frame() enricher(gene = gene_symbols_vector, TERM2GENE = msigdbr_t2g, ...) msigdbr_list <- split(x = msigdbr_df$gene_symbol, f = msigdbr_df$gs_name) fgsea(pathways = msigdbr_list, ...) msigdbr_list <- split(x = msigdbr_df$gene_symbol, f = msigdbr_df$gs_name) gsva(gset.idx.list = msigdbr_list, ...)"},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"potential-questions-or-concerns","dir":"Articles","previous_headings":"","what":"Potential questions or concerns","title":"Introduction to msigdbr","text":"version MSigDB used? package generated MSigDB v2022.1. MSigDB version used base msigdbr CRAN package version. can check installed version packageVersion(\"msigdbr\"). Can download gene sets directly MSigDB instead using package? Yes. can import GMT files (getGmt() GSEABase package, example). GMTs include human genes, even gene sets generated mouse experiments. working non-human data, convert MSigDB genes organism genes human. Can convert human mouse genes just adjusting gene capitalization? work genes, . Can convert human genes organism instead using package? Yes. popular method using biomaRt package. may still end dozens homologs genes, additional cleanup may helpful. Aren’t already similar tools? resources provide msigdbr functionality served inspiration package. WEHI provides MSigDB gene sets R format human mouse. MSigDF relies WEHI resource, converted tidyverse-friendly data frame. recent ToledoEM/msigdf fork. updated varying frequencies may based latest version MSigDB. Since 2022, GSEA/MSigDB team provides collections natively mouse don’t require orthology conversion. questions? can submit feedback report bugs GitHub.","code":""},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"details","dir":"Articles","previous_headings":"","what":"Details","title":"Introduction to msigdbr","text":"Molecular Signatures Database (MSigDB) collection gene sets originally created use Gene Set Enrichment Analysis (GSEA) software. cite use underlying MSigDB data, reference Subramanian, Tamayo, et al. (2005, PNAS) one following appropriate: Liberzon, et al. (2011, Bioinformatics), Liberzon, et al. (2015, Cell Systems), also source gene set. Gene homologs provided HUGO Gene Nomenclature Committee European Bioinformatics Institute integrates orthology assertions predicted human genes eggNOG, Ensembl Compara, HGNC, HomoloGene, Inparanoid, NCBI Gene Orthology, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, TreeFam ZFIN. human equivalent within species, ortholog supported largest number databases used. information cite cite R package msigdbr, can execute citation(\"msigdbr\").","code":""},{"path":"https://igordot.github.io/msigdbr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Igor Dolgalev. Author, maintainer.","code":""},{"path":"https://igordot.github.io/msigdbr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Dolgalev (2024). msigdbr: MSigDB Gene Sets Multiple Organisms Tidy Data Format. R package version 2022.1.1, https://igordot.github.io/msigdbr/.","code":"@Manual{,   title = {msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format},   author = {Igor Dolgalev},   year = {2024},   note = {R package version 2022.1.1},   url = {https://igordot.github.io/msigdbr/}, }"},{"path":[]},{"path":"https://igordot.github.io/msigdbr/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"MSigDB gene sets R package","text":"msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets typically used Gene Set Enrichment Analysis (GSEA) software: R-friendly “tidy” format one gene pair per row multiple frequently studied model organisms, mouse, rat, pig, zebrafish, fly, yeast, addition original human genes gene symbols well NCBI Entrez Ensembl IDs without accessing external resources requiring active internet connection","code":""},{"path":"https://igordot.github.io/msigdbr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"MSigDB gene sets R package","text":"package can installed CRAN. {r} install.packages(\"msigdbr\") Releases available CRAN can installed GitHub (specific release version can specified): {r} remotes::install_github(\"igordot/msigdbr\", ref = \"v2022.1.1\")","code":""},{"path":"https://igordot.github.io/msigdbr/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"MSigDB gene sets R package","text":"package data can accessed using msigdbr() function, returns data frame gene sets member genes. example, can retrieve mouse genes C2 (curated) CGP (chemical genetic perturbations) gene sets. {r} library(msigdbr) genesets = msigdbr(species = \"mouse\", category = \"C2\", subcategory = \"CGP\") Check documentation website information.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve the gene sets data frame — msigdbr","title":"Retrieve the gene sets data frame — msigdbr","text":"Retrieve data frame gene sets member genes. available species collections can checked msigdbr_species() msigdbr_collections().","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve the gene sets data frame — msigdbr","text":"","code":"msigdbr(species = \"Homo sapiens\", category = NULL, subcategory = NULL)"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve the gene sets data frame — msigdbr","text":"species Species name, Homo sapiens Mus musculus. category MSigDB collection abbreviation, H C1. subcategory MSigDB sub-collection abbreviation, CGP BP.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve the gene sets data frame — msigdbr","text":"data frame gene sets one gene per row.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Retrieve the gene sets data frame — msigdbr","text":"https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve the gene sets data frame — msigdbr","text":"","code":"# get all human gene sets # \\donttest{ msigdbr(species = \"Homo sapiens\") #> # A tibble: 3,995,746 × 15 #>    gs_cat gs_subcat      gs_name        gene_symbol entrez_gene ensembl_gene    #>    <chr>  <chr>          <chr>          <chr>             <int> <chr>           #>  1 C3     MIR:MIR_Legacy AAACCAC_MIR140 ABCC4             10257 ENSG00000125257 #>  2 C3     MIR:MIR_Legacy AAACCAC_MIR140 ABRAXAS2          23172 ENSG00000165660 #>  3 C3     MIR:MIR_Legacy AAACCAC_MIR140 ACTN4                81 ENSG00000130402 #>  4 C3     MIR:MIR_Legacy AAACCAC_MIR140 ACVR1                90 ENSG00000115170 #>  5 C3     MIR:MIR_Legacy AAACCAC_MIR140 ADAM9              8754 ENSG00000168615 #>  6 C3     MIR:MIR_Legacy AAACCAC_MIR140 ADAMTS5           11096 ENSG00000154736 #>  7 C3     MIR:MIR_Legacy AAACCAC_MIR140 AMER2            219287 ENSG00000165566 #>  8 C3     MIR:MIR_Legacy AAACCAC_MIR140 ANK2                287 ENSG00000145362 #>  9 C3     MIR:MIR_Legacy AAACCAC_MIR140 API5               8539 ENSG00000166181 #> 10 C3     MIR:MIR_Legacy AAACCAC_MIR140 BACH1               571 ENSG00000156273 #> # ℹ 3,995,736 more rows #> # ℹ 9 more variables: human_gene_symbol <chr>, human_entrez_gene <int>, #> #   human_ensembl_gene <chr>, gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, #> #   gs_exact_source <chr>, gs_url <chr>, gs_description <chr> # }  # get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets # \\donttest{ msigdbr(species = \"Mus musculus\", category = \"C2\", subcategory = \"CGP\") #> # A tibble: 378,755 × 18 #>    gs_cat gs_subcat gs_name                 gene_symbol entrez_gene ensembl_gene #>    <chr>  <chr>     <chr>                   <chr>             <int> <chr>        #>  1 C2     CGP       ABBUD_LIF_SIGNALING_1_… Ahnak             66395 ENSMUSG0000… #>  2 C2     CGP       ABBUD_LIF_SIGNALING_1_… Alcam             11658 ENSMUSG0000… #>  3 C2     CGP       ABBUD_LIF_SIGNALING_1_… Ankrd40           71452 ENSMUSG0000… #>  4 C2     CGP       ABBUD_LIF_SIGNALING_1_… Arid1a            93760 ENSMUSG0000… #>  5 C2     CGP       ABBUD_LIF_SIGNALING_1_… Bckdhb            12040 ENSMUSG0000… #>  6 C2     CGP       ABBUD_LIF_SIGNALING_1_… AU021092         239691 ENSMUSG0000… #>  7 C2     CGP       ABBUD_LIF_SIGNALING_1_… Capn9             73647 ENSMUSG0000… #>  8 C2     CGP       ABBUD_LIF_SIGNALING_1_… Cd24a             12484 ENSMUSG0000… #>  9 C2     CGP       ABBUD_LIF_SIGNALING_1_… Cyfip1            20430 ENSMUSG0000… #> 10 C2     CGP       ABBUD_LIF_SIGNALING_1_… Dcaf11            28199 ENSMUSG0000… #> # ℹ 378,745 more rows #> # ℹ 12 more variables: human_gene_symbol <chr>, human_entrez_gene <int>, #> #   human_ensembl_gene <chr>, gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, #> #   gs_exact_source <chr>, gs_url <chr>, gs_description <chr>, taxon_id <int>, #> #   ortholog_sources <chr>, num_ortholog_sources <dbl> # }"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_collections.html","id":null,"dir":"Reference","previous_headings":"","what":"List the collections available in the msigdbr package — msigdbr_collections","title":"List the collections available in the msigdbr package — msigdbr_collections","text":"List collections available msigdbr package","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_collections.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List the collections available in the msigdbr package — msigdbr_collections","text":"","code":"msigdbr_collections()"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_collections.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List the collections available in the msigdbr package — msigdbr_collections","text":"data frame available collections.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_collections.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List the collections available in the msigdbr package — msigdbr_collections","text":"","code":"msigdbr_collections() #> # A tibble: 23 × 3 #>    gs_cat gs_subcat         num_genesets #>    <chr>  <chr>                    <int> #>  1 C1     \"\"                         299 #>  2 C2     \"CGP\"                     3399 #>  3 C2     \"CP\"                        29 #>  4 C2     \"CP:BIOCARTA\"              292 #>  5 C2     \"CP:KEGG\"                  186 #>  6 C2     \"CP:PID\"                   196 #>  7 C2     \"CP:REACTOME\"             1635 #>  8 C2     \"CP:WIKIPATHWAYS\"          712 #>  9 C3     \"MIR:MIRDB\"               2377 #> 10 C3     \"MIR:MIR_Legacy\"           221 #> # ℹ 13 more rows"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_show_species.html","id":null,"dir":"Reference","previous_headings":"","what":"List the species available in the msigdbr package — msigdbr_show_species","title":"List the species available in the msigdbr package — msigdbr_show_species","text":"function deprecated replaced msigdbr_species().","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_show_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List the species available in the msigdbr package — msigdbr_show_species","text":"","code":"msigdbr_show_species()"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_show_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List the species available in the msigdbr package — msigdbr_show_species","text":"vector possible species.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_species.html","id":null,"dir":"Reference","previous_headings":"","what":"List the species available in the msigdbr package — msigdbr_species","title":"List the species available in the msigdbr package — msigdbr_species","text":"List species available msigdbr package","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List the species available in the msigdbr package — msigdbr_species","text":"","code":"msigdbr_species()"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List the species available in the msigdbr package — msigdbr_species","text":"data frame available species.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_species.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List the species available in the msigdbr package — msigdbr_species","text":"","code":"msigdbr_species() #> # A tibble: 20 × 2 #>    species_name                    species_common_name                           #>    <chr>                           <chr>                                         #>  1 Anolis carolinensis             Carolina anole, green anole                   #>  2 Bos taurus                      bovine, cattle, cow, dairy cow, domestic cat… #>  3 Caenorhabditis elegans          NA                                            #>  4 Canis lupus familiaris          dog, dogs                                     #>  5 Danio rerio                     leopard danio, zebra danio, zebra fish, zebr… #>  6 Drosophila melanogaster         fruit fly                                     #>  7 Equus caballus                  domestic horse, equine, horse                 #>  8 Felis catus                     cat, cats, domestic cat                       #>  9 Gallus gallus                   bantam, chicken, chickens, Gallus domesticus  #> 10 Homo sapiens                    human                                         #> 11 Macaca mulatta                  rhesus macaque, rhesus macaques, Rhesus monk… #> 12 Monodelphis domestica           gray short-tailed opossum                     #> 13 Mus musculus                    house mouse, mouse                            #> 14 Ornithorhynchus anatinus        duck-billed platypus, duckbill platypus, pla… #> 15 Pan troglodytes                 chimpanzee                                    #> 16 Rattus norvegicus               brown rat, Norway rat, rat, rats              #> 17 Saccharomyces cerevisiae        baker's yeast, brewer's yeast, S. cerevisiae  #> 18 Schizosaccharomyces pombe 972h- NA                                            #> 19 Sus scrofa                      pig, pigs, swine, wild boar                   #> 20 Xenopus tropicalis              tropical clawed frog, western clawed frog"},{"path":"https://igordot.github.io/msigdbr/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://igordot.github.io/msigdbr/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-202211","dir":"Changelog","previous_headings":"","what":"msigdbr 2022.1.1","title":"msigdbr 2022.1.1","text":"Based MSigDB v2022.1 release. CRAN.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-751","dir":"Changelog","previous_headings":"","what":"msigdbr 7.5.1","title":"msigdbr 7.5.1","text":"CRAN release: 2022-03-30 Based MSigDB v7.5.1 release.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-741","dir":"Changelog","previous_headings":"","what":"msigdbr 7.4.1","title":"msigdbr 7.4.1","text":"CRAN release: 2021-05-05 Based MSigDB v7.4 release. Added Ensembl gene IDs returned gene sets.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-721","dir":"Changelog","previous_headings":"","what":"msigdbr 7.2.1","title":"msigdbr 7.2.1","text":"CRAN release: 2020-10-02 Based MSigDB v7.2 release. Added annotation fields returned gene sets. Added msigdbr_species() alternative msigdbr_show_species(). Added msigdbr_collections().","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-711","dir":"Changelog","previous_headings":"","what":"msigdbr 7.1.1","title":"msigdbr 7.1.1","text":"CRAN release: 2020-05-14 Based MSigDB v7.1 release. Increased ortholog prediction stringency.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-701","dir":"Changelog","previous_headings":"","what":"msigdbr 7.0.1","title":"msigdbr 7.0.1","text":"CRAN release: 2019-09-04 Based MSigDB v7.0 release. Fixed output selecting multiple collections.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-621","dir":"Changelog","previous_headings":"","what":"msigdbr 6.2.1","title":"msigdbr 6.2.1","text":"CRAN release: 2018-10-09 Based MSigDB v6.2 release.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-611","dir":"Changelog","previous_headings":"","what":"msigdbr 6.1.1","title":"msigdbr 6.1.1","text":"CRAN release: 2018-04-12 Based MSigDB v6.1 release. Initial CRAN submission.","code":""}]
+[{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to msigdbr","text":"Pathway analysis common task genomics research many available R-based software tools. Depending tool, may necessary import pathways, translate genes appropriate species, convert symbols IDs, format resulting object. msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets typically used Gene Set Enrichment Analysis (GSEA) software: R-friendly “tidy” format one gene pair per row multiple frequently studied model organisms, mouse, rat, pig, zebrafish, fly, yeast, addition original human genes gene symbols well NCBI Entrez Ensembl IDs without accessing external resources requiring active internet connection Please aware homologs computationally predicted distinct genes. full pathways may well conserved across species.","code":""},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to msigdbr","text":"package can installed CRAN.","code":"install.packages(\"msigdbr\")"},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"usage","dir":"Articles","previous_headings":"","what":"Usage","title":"Introduction to msigdbr","text":"Load package. gene sets database can retrieved specifying species interest. can retrieve data just specific collection/category, hallmark gene sets. can specify sub-category, C2 (curated) CGP (chemical genetic perturbations) gene sets. require custom filtering, msigdbr() function output data frame can manipulated using standard methods. example, can subset specific collection/category using dplyr::filter().","code":"library(msigdbr) #> Error in get(paste0(generic, \".\", class), envir = get_method_env()) :  #>   object 'type_sum.accel' not found all_gene_sets <- msigdbr(species = \"Mus musculus\") head(all_gene_sets) #> # A tibble: 6 × 18 #>   gs_cat gs_subcat     gs_name gene_symbol entrez_gene ensembl_gene human_gene…¹ #>   <chr>  <chr>         <chr>   <chr>             <int> <chr>        <chr>        #> 1 C3     MIR:MIR_LEGA… AAACCA… Abcc4            239273 ENSMUSG0000… ABCC4        #> 2 C3     MIR:MIR_LEGA… AAACCA… Abraxas2         109359 ENSMUSG0000… ABRAXAS2     #> 3 C3     MIR:MIR_LEGA… AAACCA… Actn4             60595 ENSMUSG0000… ACTN4        #> 4 C3     MIR:MIR_LEGA… AAACCA… Acvr1             11477 ENSMUSG0000… ACVR1        #> 5 C3     MIR:MIR_LEGA… AAACCA… Adam9             11502 ENSMUSG0000… ADAM9        #> 6 C3     MIR:MIR_LEGA… AAACCA… Adamts5           23794 ENSMUSG0000… ADAMTS5      #> # ℹ abbreviated name: ¹​human_gene_symbol #> # ℹ 11 more variables: human_entrez_gene <int>, human_ensembl_gene <chr>, #> #   gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, gs_exact_source <chr>, #> #   gs_url <chr>, gs_description <chr>, taxon_id <int>, ortholog_sources <chr>, #> #   num_ortholog_sources <dbl> h_gene_sets <- msigdbr(species = \"mouse\", category = \"H\") head(h_gene_sets) #> # A tibble: 6 × 18 #>   gs_cat gs_subcat gs_name     gene_symbol entrez_gene ensembl_gene human_gene…¹ #>   <chr>  <chr>     <chr>       <chr>             <int> <chr>        <chr>        #> 1 H      \"\"        HALLMARK_A… Abca1             11303 ENSMUSG0000… ABCA1        #> 2 H      \"\"        HALLMARK_A… Abcb8             74610 ENSMUSG0000… ABCB8        #> 3 H      \"\"        HALLMARK_A… Acaa2             52538 ENSMUSG0000… ACAA2        #> 4 H      \"\"        HALLMARK_A… Acadl             11363 ENSMUSG0000… ACADL        #> 5 H      \"\"        HALLMARK_A… Acadm             11364 ENSMUSG0000… ACADM        #> 6 H      \"\"        HALLMARK_A… Acads             11409 ENSMUSG0000… ACADS        #> # ℹ abbreviated name: ¹​human_gene_symbol #> # ℹ 11 more variables: human_entrez_gene <int>, human_ensembl_gene <chr>, #> #   gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, gs_exact_source <chr>, #> #   gs_url <chr>, gs_description <chr>, taxon_id <int>, ortholog_sources <chr>, #> #   num_ortholog_sources <dbl> cgp_gene_sets <- msigdbr(species = \"mouse\", category = \"C2\", subcategory = \"CGP\") head(cgp_gene_sets) #> # A tibble: 6 × 18 #>   gs_cat gs_subcat gs_name     gene_symbol entrez_gene ensembl_gene human_gene…¹ #>   <chr>  <chr>     <chr>       <chr>             <int> <chr>        <chr>        #> 1 C2     CGP       ABBUD_LIF_… Ahnak             66395 ENSMUSG0000… AHNAK        #> 2 C2     CGP       ABBUD_LIF_… Alcam             11658 ENSMUSG0000… ALCAM        #> 3 C2     CGP       ABBUD_LIF_… Ankrd40           71452 ENSMUSG0000… ANKRD40      #> 4 C2     CGP       ABBUD_LIF_… Arid1a            93760 ENSMUSG0000… ARID1A       #> 5 C2     CGP       ABBUD_LIF_… Bckdhb            12040 ENSMUSG0000… BCKDHB       #> 6 C2     CGP       ABBUD_LIF_… AU021092         239691 ENSMUSG0000… C16orf89     #> # ℹ abbreviated name: ¹​human_gene_symbol #> # ℹ 11 more variables: human_entrez_gene <int>, human_ensembl_gene <chr>, #> #   gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, gs_exact_source <chr>, #> #   gs_url <chr>, gs_description <chr>, taxon_id <int>, ortholog_sources <chr>, #> #   num_ortholog_sources <dbl> all_gene_sets %>%   dplyr::filter(gs_cat == \"H\") %>%   head() #> # A tibble: 6 × 18 #>   gs_cat gs_subcat gs_name     gene_symbol entrez_gene ensembl_gene human_gene…¹ #>   <chr>  <chr>     <chr>       <chr>             <int> <chr>        <chr>        #> 1 H      \"\"        HALLMARK_A… Abca1             11303 ENSMUSG0000… ABCA1        #> 2 H      \"\"        HALLMARK_A… Abcb8             74610 ENSMUSG0000… ABCB8        #> 3 H      \"\"        HALLMARK_A… Acaa2             52538 ENSMUSG0000… ACAA2        #> 4 H      \"\"        HALLMARK_A… Acadl             11363 ENSMUSG0000… ACADL        #> 5 H      \"\"        HALLMARK_A… Acadm             11364 ENSMUSG0000… ACADM        #> 6 H      \"\"        HALLMARK_A… Acads             11409 ENSMUSG0000… ACADS        #> # ℹ abbreviated name: ¹​human_gene_symbol #> # ℹ 11 more variables: human_entrez_gene <int>, human_ensembl_gene <chr>, #> #   gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, gs_exact_source <chr>, #> #   gs_url <chr>, gs_description <chr>, taxon_id <int>, ortholog_sources <chr>, #> #   num_ortholog_sources <dbl>"},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"helper-functions","dir":"Articles","previous_headings":"","what":"Helper functions","title":"Introduction to msigdbr","text":"msigdbr_species() msigdbr_collections() helper functions assist setting msigdbr() parameters. can check available species msigdbr_species(). Either scientific common names acceptable msigdbr() function. can check available collections msigdbr_collections().","code":"msigdbr_species() #> # A tibble: 20 × 2 #>    species_name                    species_common_name                           #>    <chr>                           <chr>                                         #>  1 Anolis carolinensis             Carolina anole, green anole                   #>  2 Bos taurus                      bovine, cattle, cow, dairy cow, domestic cat… #>  3 Caenorhabditis elegans          NA                                            #>  4 Canis lupus familiaris          dog, dogs                                     #>  5 Danio rerio                     leopard danio, zebra danio, zebra fish, zebr… #>  6 Drosophila melanogaster         fruit fly                                     #>  7 Equus caballus                  domestic horse, equine, horse                 #>  8 Felis catus                     cat, cats, domestic cat                       #>  9 Gallus gallus                   bantam, chicken, chickens, Gallus domesticus  #> 10 Homo sapiens                    human                                         #> 11 Macaca mulatta                  rhesus macaque, rhesus macaques, Rhesus monk… #> 12 Monodelphis domestica           gray short-tailed opossum                     #> 13 Mus musculus                    house mouse, mouse                            #> 14 Ornithorhynchus anatinus        duck-billed platypus, duckbill platypus, pla… #> 15 Pan troglodytes                 chimpanzee                                    #> 16 Rattus norvegicus               brown rat, Norway rat, rat, rats              #> 17 Saccharomyces cerevisiae        baker's yeast, brewer's yeast, S. cerevisiae  #> 18 Schizosaccharomyces pombe 972h- NA                                            #> 19 Sus scrofa                      pig, pigs, swine, wild boar                   #> 20 Xenopus tropicalis              tropical clawed frog, western clawed frog msigdbr_collections() #> # A tibble: 23 × 3 #>    gs_cat gs_subcat         num_genesets #>    <chr>  <chr>                    <int> #>  1 C1     \"\"                         300 #>  2 C2     \"CGP\"                     3405 #>  3 C2     \"CP\"                        29 #>  4 C2     \"CP:BIOCARTA\"              292 #>  5 C2     \"CP:KEGG\"                  186 #>  6 C2     \"CP:PID\"                   196 #>  7 C2     \"CP:REACTOME\"             1654 #>  8 C2     \"CP:WIKIPATHWAYS\"          733 #>  9 C3     \"MIR:MIRDB\"               2377 #> 10 C3     \"MIR:MIR_LEGACY\"           221 #> 11 C3     \"TFT:GTRD\"                 505 #> 12 C3     \"TFT:TFT_LEGACY\"           610 #> 13 C4     \"CGN\"                      427 #> 14 C4     \"CM\"                       431 #> 15 C5     \"GO:BP\"                   7751 #> 16 C5     \"GO:CC\"                   1009 #> 17 C5     \"GO:MF\"                   1772 #> 18 C5     \"HPO\"                     5405 #> 19 C6     \"\"                         189 #> 20 C7     \"IMMUNESIGDB\"             4872 #> 21 C7     \"VAX\"                      347 #> 22 C8     \"\"                         830 #> 23 H      \"\"                          50"},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"pathway-enrichment-analysis","dir":"Articles","previous_headings":"","what":"Pathway enrichment analysis","title":"Introduction to msigdbr","text":"msigdbr output can used various pathway analysis packages. Use gene sets data frame clusterProfiler genes Entrez Gene IDs. Use gene sets data frame clusterProfiler genes gene symbols. Use gene sets data frame fgsea. Use gene sets data frame GSVA.","code":"msigdbr_t2g <- msigdbr_df %>%   dplyr::distinct(gs_name, entrez_gene) %>%   as.data.frame() enricher(gene = gene_ids_vector, TERM2GENE = msigdbr_t2g, ...) msigdbr_t2g <- msigdbr_df %>%   dplyr::distinct(gs_name, gene_symbol) %>%   as.data.frame() enricher(gene = gene_symbols_vector, TERM2GENE = msigdbr_t2g, ...) msigdbr_list <- split(x = msigdbr_df$gene_symbol, f = msigdbr_df$gs_name) fgsea(pathways = msigdbr_list, ...) msigdbr_list <- split(x = msigdbr_df$gene_symbol, f = msigdbr_df$gs_name) gsva(gset.idx.list = msigdbr_list, ...)"},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"potential-questions-or-concerns","dir":"Articles","previous_headings":"","what":"Potential questions or concerns","title":"Introduction to msigdbr","text":"version MSigDB used? package generated MSigDB v2023.1.Hs. MSigDB version used base msigdbr CRAN package version. can check installed version packageVersion(\"msigdbr\"). Can download gene sets directly MSigDB instead using package? Yes. can import GMT files (getGmt() GSEABase package, example). GMTs include human genes, even gene sets generated mouse experiments. working non-human data, convert MSigDB genes organism genes human. Can convert human mouse genes just adjusting gene capitalization? work genes, . Can convert human genes organism instead using package? Yes. popular method using biomaRt package. may still end dozens homologs genes, additional cleanup may helpful. Aren’t already similar tools? resources provide msigdbr functionality served inspiration package. WEHI provides MSigDB gene sets R format human mouse. MSigDF relies WEHI resource, converted tidyverse-friendly data frame. recent ToledoEM/msigdf fork. updated varying frequencies may based latest version MSigDB. Since 2022, GSEA/MSigDB team provides collections natively mouse don’t require orthology conversion. questions? can submit feedback report bugs GitHub.","code":""},{"path":"https://igordot.github.io/msigdbr/articles/msigdbr-intro.html","id":"details","dir":"Articles","previous_headings":"","what":"Details","title":"Introduction to msigdbr","text":"Molecular Signatures Database (MSigDB) collection gene sets originally created use Gene Set Enrichment Analysis (GSEA) software. cite use underlying MSigDB data, reference Subramanian, Tamayo, et al. (2005, PNAS) one following appropriate: Liberzon, et al. (2011, Bioinformatics), Liberzon, et al. (2015, Cell Systems), also source gene set. Gene homologs provided HUGO Gene Nomenclature Committee European Bioinformatics Institute integrates orthology assertions predicted human genes eggNOG, Ensembl Compara, HGNC, HomoloGene, Inparanoid, NCBI Gene Orthology, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, TreeFam ZFIN. human equivalent within species, ortholog supported largest number databases used. information cite cite R package msigdbr, can execute citation(\"msigdbr\").","code":""},{"path":"https://igordot.github.io/msigdbr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Igor Dolgalev. Author, maintainer.","code":""},{"path":"https://igordot.github.io/msigdbr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Dolgalev (2024). msigdbr: MSigDB Gene Sets Multiple Organisms Tidy Data Format. R package version 2023.1.1, https://igordot.github.io/msigdbr/.","code":"@Manual{,   title = {msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format},   author = {Igor Dolgalev},   year = {2024},   note = {R package version 2023.1.1},   url = {https://igordot.github.io/msigdbr/}, }"},{"path":[]},{"path":"https://igordot.github.io/msigdbr/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"MSigDB gene sets R package","text":"msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets typically used Gene Set Enrichment Analysis (GSEA) software: R-friendly “tidy” format one gene pair per row multiple frequently studied model organisms, mouse, rat, pig, zebrafish, fly, yeast, addition original human genes gene symbols well NCBI Entrez Ensembl IDs without accessing external resources requiring active internet connection","code":""},{"path":"https://igordot.github.io/msigdbr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"MSigDB gene sets R package","text":"package can installed CRAN. {r} install.packages(\"msigdbr\") Releases available CRAN can installed GitHub (specific release version can specified): {r} remotes::install_github(\"igordot/msigdbr\", ref = \"v2022.1.1\")","code":""},{"path":"https://igordot.github.io/msigdbr/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"MSigDB gene sets R package","text":"package data can accessed using msigdbr() function, returns data frame gene sets member genes. example, can retrieve mouse genes C2 (curated) CGP (chemical genetic perturbations) gene sets. {r} library(msigdbr) genesets = msigdbr(species = \"mouse\", category = \"C2\", subcategory = \"CGP\") Check documentation website information.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve the gene sets data frame — msigdbr","title":"Retrieve the gene sets data frame — msigdbr","text":"Retrieve data frame gene sets member genes. available species collections can checked msigdbr_species() msigdbr_collections().","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve the gene sets data frame — msigdbr","text":"","code":"msigdbr(species = \"Homo sapiens\", category = NULL, subcategory = NULL)"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve the gene sets data frame — msigdbr","text":"species Species name, Homo sapiens Mus musculus. category MSigDB collection abbreviation, H C1. subcategory MSigDB sub-collection abbreviation, CGP BP.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve the gene sets data frame — msigdbr","text":"data frame gene sets one gene per row.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Retrieve the gene sets data frame — msigdbr","text":"https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve the gene sets data frame — msigdbr","text":"","code":"# get all human gene sets # \\donttest{ msigdbr(species = \"Homo sapiens\") #> # A tibble: 4,029,754 × 15 #>    gs_cat gs_subcat      gs_name        gene_symbol entrez_gene ensembl_gene    #>    <chr>  <chr>          <chr>          <chr>             <int> <chr>           #>  1 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ABCC4             10257 ENSG00000125257 #>  2 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ABRAXAS2          23172 ENSG00000165660 #>  3 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ACTN4                81 ENSG00000130402 #>  4 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ACVR1                90 ENSG00000115170 #>  5 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ADAM9              8754 ENSG00000168615 #>  6 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ADAMTS5           11096 ENSG00000154736 #>  7 C3     MIR:MIR_LEGACY AAACCAC_MIR140 AMER2            219287 ENSG00000165566 #>  8 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ANK2                287 ENSG00000145362 #>  9 C3     MIR:MIR_LEGACY AAACCAC_MIR140 API5               8539 ENSG00000166181 #> 10 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ATOSA             56204 ENSG00000047346 #> # ℹ 4,029,744 more rows #> # ℹ 9 more variables: human_gene_symbol <chr>, human_entrez_gene <int>, #> #   human_ensembl_gene <chr>, gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, #> #   gs_exact_source <chr>, gs_url <chr>, gs_description <chr> # }  # get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets # \\donttest{ msigdbr(species = \"Mus musculus\", category = \"C2\", subcategory = \"CGP\") #> # A tibble: 378,935 × 18 #>    gs_cat gs_subcat gs_name                 gene_symbol entrez_gene ensembl_gene #>    <chr>  <chr>     <chr>                   <chr>             <int> <chr>        #>  1 C2     CGP       ABBUD_LIF_SIGNALING_1_… Ahnak             66395 ENSMUSG0000… #>  2 C2     CGP       ABBUD_LIF_SIGNALING_1_… Alcam             11658 ENSMUSG0000… #>  3 C2     CGP       ABBUD_LIF_SIGNALING_1_… Ankrd40           71452 ENSMUSG0000… #>  4 C2     CGP       ABBUD_LIF_SIGNALING_1_… Arid1a            93760 ENSMUSG0000… #>  5 C2     CGP       ABBUD_LIF_SIGNALING_1_… Bckdhb            12040 ENSMUSG0000… #>  6 C2     CGP       ABBUD_LIF_SIGNALING_1_… AU021092         239691 ENSMUSG0000… #>  7 C2     CGP       ABBUD_LIF_SIGNALING_1_… Capn9             73647 ENSMUSG0000… #>  8 C2     CGP       ABBUD_LIF_SIGNALING_1_… Cd24a             12484 ENSMUSG0000… #>  9 C2     CGP       ABBUD_LIF_SIGNALING_1_… Cyfip1            20430 ENSMUSG0000… #> 10 C2     CGP       ABBUD_LIF_SIGNALING_1_… Dcaf11            28199 ENSMUSG0000… #> # ℹ 378,925 more rows #> # ℹ 12 more variables: human_gene_symbol <chr>, human_entrez_gene <int>, #> #   human_ensembl_gene <chr>, gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>, #> #   gs_exact_source <chr>, gs_url <chr>, gs_description <chr>, taxon_id <int>, #> #   ortholog_sources <chr>, num_ortholog_sources <dbl> # }"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_collections.html","id":null,"dir":"Reference","previous_headings":"","what":"List the collections available in the msigdbr package — msigdbr_collections","title":"List the collections available in the msigdbr package — msigdbr_collections","text":"List collections available msigdbr package","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_collections.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List the collections available in the msigdbr package — msigdbr_collections","text":"","code":"msigdbr_collections()"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_collections.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List the collections available in the msigdbr package — msigdbr_collections","text":"data frame available collections.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_collections.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List the collections available in the msigdbr package — msigdbr_collections","text":"","code":"msigdbr_collections() #> # A tibble: 23 × 3 #>    gs_cat gs_subcat         num_genesets #>    <chr>  <chr>                    <int> #>  1 C1     \"\"                         300 #>  2 C2     \"CGP\"                     3405 #>  3 C2     \"CP\"                        29 #>  4 C2     \"CP:BIOCARTA\"              292 #>  5 C2     \"CP:KEGG\"                  186 #>  6 C2     \"CP:PID\"                   196 #>  7 C2     \"CP:REACTOME\"             1654 #>  8 C2     \"CP:WIKIPATHWAYS\"          733 #>  9 C3     \"MIR:MIRDB\"               2377 #> 10 C3     \"MIR:MIR_LEGACY\"           221 #> # ℹ 13 more rows"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_show_species.html","id":null,"dir":"Reference","previous_headings":"","what":"List the species available in the msigdbr package — msigdbr_show_species","title":"List the species available in the msigdbr package — msigdbr_show_species","text":"function deprecated replaced msigdbr_species().","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_show_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List the species available in the msigdbr package — msigdbr_show_species","text":"","code":"msigdbr_show_species()"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_show_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List the species available in the msigdbr package — msigdbr_show_species","text":"vector possible species.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_species.html","id":null,"dir":"Reference","previous_headings":"","what":"List the species available in the msigdbr package — msigdbr_species","title":"List the species available in the msigdbr package — msigdbr_species","text":"List species available msigdbr package","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List the species available in the msigdbr package — msigdbr_species","text":"","code":"msigdbr_species()"},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List the species available in the msigdbr package — msigdbr_species","text":"data frame available species.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/msigdbr_species.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List the species available in the msigdbr package — msigdbr_species","text":"","code":"msigdbr_species() #> # A tibble: 20 × 2 #>    species_name                    species_common_name                           #>    <chr>                           <chr>                                         #>  1 Anolis carolinensis             Carolina anole, green anole                   #>  2 Bos taurus                      bovine, cattle, cow, dairy cow, domestic cat… #>  3 Caenorhabditis elegans          NA                                            #>  4 Canis lupus familiaris          dog, dogs                                     #>  5 Danio rerio                     leopard danio, zebra danio, zebra fish, zebr… #>  6 Drosophila melanogaster         fruit fly                                     #>  7 Equus caballus                  domestic horse, equine, horse                 #>  8 Felis catus                     cat, cats, domestic cat                       #>  9 Gallus gallus                   bantam, chicken, chickens, Gallus domesticus  #> 10 Homo sapiens                    human                                         #> 11 Macaca mulatta                  rhesus macaque, rhesus macaques, Rhesus monk… #> 12 Monodelphis domestica           gray short-tailed opossum                     #> 13 Mus musculus                    house mouse, mouse                            #> 14 Ornithorhynchus anatinus        duck-billed platypus, duckbill platypus, pla… #> 15 Pan troglodytes                 chimpanzee                                    #> 16 Rattus norvegicus               brown rat, Norway rat, rat, rats              #> 17 Saccharomyces cerevisiae        baker's yeast, brewer's yeast, S. cerevisiae  #> 18 Schizosaccharomyces pombe 972h- NA                                            #> 19 Sus scrofa                      pig, pigs, swine, wild boar                   #> 20 Xenopus tropicalis              tropical clawed frog, western clawed frog"},{"path":"https://igordot.github.io/msigdbr/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://igordot.github.io/msigdbr/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://igordot.github.io/msigdbr/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-202311","dir":"Changelog","previous_headings":"","what":"msigdbr 2023.1.1","title":"msigdbr 2023.1.1","text":"Based MSigDB v2023.1.Hs release. CRAN.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-202211","dir":"Changelog","previous_headings":"","what":"msigdbr 2022.1.1","title":"msigdbr 2022.1.1","text":"Based MSigDB v2022.1.Hs release. CRAN.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-751","dir":"Changelog","previous_headings":"","what":"msigdbr 7.5.1","title":"msigdbr 7.5.1","text":"CRAN release: 2022-03-30 Based MSigDB v7.5.1 release.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-741","dir":"Changelog","previous_headings":"","what":"msigdbr 7.4.1","title":"msigdbr 7.4.1","text":"CRAN release: 2021-05-05 Based MSigDB v7.4 release. Added Ensembl gene IDs returned gene sets.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-721","dir":"Changelog","previous_headings":"","what":"msigdbr 7.2.1","title":"msigdbr 7.2.1","text":"CRAN release: 2020-10-02 Based MSigDB v7.2 release. Added annotation fields returned gene sets. Added msigdbr_species() alternative msigdbr_show_species(). Added msigdbr_collections().","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-711","dir":"Changelog","previous_headings":"","what":"msigdbr 7.1.1","title":"msigdbr 7.1.1","text":"CRAN release: 2020-05-14 Based MSigDB v7.1 release. Increased ortholog prediction stringency.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-701","dir":"Changelog","previous_headings":"","what":"msigdbr 7.0.1","title":"msigdbr 7.0.1","text":"CRAN release: 2019-09-04 Based MSigDB v7.0 release. Fixed output selecting multiple collections.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-621","dir":"Changelog","previous_headings":"","what":"msigdbr 6.2.1","title":"msigdbr 6.2.1","text":"CRAN release: 2018-10-09 Based MSigDB v6.2 release.","code":""},{"path":"https://igordot.github.io/msigdbr/news/index.html","id":"msigdbr-611","dir":"Changelog","previous_headings":"","what":"msigdbr 6.1.1","title":"msigdbr 6.1.1","text":"CRAN release: 2018-04-12 Based MSigDB v6.1 release. Initial CRAN submission.","code":""}]