From 2729b77bf4d94fe6ac74bfa307d1eefb5bba0231 Mon Sep 17 00:00:00 2001 From: Anka Date: Mon, 6 Jan 2025 12:50:39 +0000 Subject: [PATCH] Built site for eisaR@1.19.0: 8254299 --- articles/eisaR.html | 155 ++++++++++++++++---------------- articles/rna-velocity.html | 132 ++++++++++++++------------- pkgdown.yml | 4 +- reference/exportToGtf.html | 1 + reference/getFeatureRanges.html | 16 +++- reference/getTx2Gene.html | 1 + 6 files changed, 162 insertions(+), 147 deletions(-) diff --git a/articles/eisaR.html b/articles/eisaR.html index fe45347..52fcf97 100644 --- a/articles/eisaR.html +++ b/articles/eisaR.html @@ -88,7 +88,7 @@

Using eisaR for Exon-Intron Split Analysis

Michael Stadler

-

2024-10-29

+

2025-01-06

Source: vignettes/eisaR.Rmd @@ -117,7 +117,7 @@

IntroductionQuasR +Bioconductor annotation and the QuasR package. It is also possible to obtain count tables for exons and introns using some other pipeline or approach, and directly start with step 3.

@@ -139,17 +139,17 @@

Preparing the annotationTxDb.Mmusculus.UCSC.mm10.knownGene -or EnsDb.Hsapiens.v86. +EnsDb objects, e.g. via packages such as TxDb.Mmusculus.UCSC.mm10.knownGene +or EnsDb.Hsapiens.v86. You can see available annotations using the following code:

pkgs <- c(BiocManager::available("TxDb")
           BiocManager::available("EnsDb"))

If you would like to use an alternative source of gene annotations, you might still be able to use eisaR by first converting your annotations into a TxDb or an EnsDb (for -creating a TxDb see makeTxDb in the txdbmaker +creating a TxDb see makeTxDb in the txdbmaker package, for creating an EnsDb see -makeEnsembldbPackage in the ensembldb +makeEnsembldbPackage in the ensembldb package).

For this example, eisaR contains a small TxDb to illustrate how regions are extracted. We will load @@ -208,7 +208,7 @@

Preparing the annotationrtracklayer +example, you can use rtracklayer to export the regions in regS into .gtf files:

@@ -219,23 +219,25 @@ 
Preparing the annotation
 
Quantify RNA-seq alignments in exons and introns
 

-
For this example we will use the QuasR
+
For this example we will use the QuasR
 package for indexing and alignment of short reads, and a small RNA-seq
 dataset that is contained in that package. As mentioned, it is also
 possible to align or also quantify your reads using an alternative
 aligner/counter, and skip over these steps. For more details about the
-syntax, we refer to the documentation and vignette of the QuasR
+syntax, we refer to the documentation and vignette of the QuasR
 package.

 

 
Align reads
 

-
Let’s first copy the sample data from the QuasR
+
Let’s first copy the sample data from the QuasR
 package to the current working directory, all contained in a folder
 named extdata:

 
 library(QuasR)
 #> Loading required package: parallel
 #> Loading required package: Rbowtie
+#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
+#>   object 'type_sum.accel' not found
 file.copy(system.file(package = "QuasR", "extdata"), ".", recursive = TRUE)
 #> [1] TRUE

 
We next align the reads to a mini-genome (fasta file
@@ -265,9 +267,9 @@ 
Align reads#> Testing the compute nodes...OK
 #> Loading QuasR on the compute nodes...preparing to run on 1 nodes...done
 #> Available cores:
-#> Mac-1730219867655.local: 1
+#> Mac-1736166207550.local: 1
 #> Performing genomic alignments for 4 samples. See progress in the log file:
-#> /Users/runner/work/eisaR/eisaR/vignettes/QuasR_log_654e6f91f14f.txt
+#> /Users/runner/work/eisaR/eisaR/vignettes/QuasR_log_ff87da4fee5.txt
 #> Genomic alignments have been created successfully
 alignmentStats(proj)
 #>                seqlength mapped unmapped
@@ -370,7 +372,7 @@ 
Alternative implementations of EISA
 
  • 
 TRUE (default): use a model adjusting for the baseline
 differences among samples, and with condition-specific region effects
-(similar to the model described in section 3.5 of the edgeR user
+(similar to the model described in section 3.5 of the edgeR user
 guide)
    • 
 
 
@@ -496,7 +498,7 @@ 
    Alternative implementations of EISA
 #> logical      46      93
 
 # comparison of deltas
-ids <- intersect(rownames(res1$DGEList), rownames(res2$DGEList))
+ids <- intersect(rownames(res1$DGEList), rownames(res2$DGEList))
 cor(res1$contrasts[ids,"Dex"], res2$contrasts[ids,"Dex"])
 #> [1] 0.989731
 cor(res1$contrasts[ids,"Din"], res2$contrasts[ids,"Din"])
@@ -531,7 +533,7 @@ 
    On
 That sample factor is nested in the condition factor (no sample can
 belong to more than one condition). Thus, we are in the situation
 described in section 3.5 (‘Comparisons both between and within
-subjects’) of the edgeR user
+subjects’) of the edgeR user
 guide, and we use the approach described there to define a design matrix
 with sample-specific baseline effects as well as condition-specific
 region effects.
    
@@ -550,7 +552,7 @@ 
    On
 #> filtering quantifyable genes...keeping 11759 from 20288 (58%)
 #> fitting statistical model...done
 #> calculating log-fold changes...done
-ids <- intersect(rownames(res3$contrasts), rownames(res4$contrasts))
+ids <- intersect(rownames(res3$contrasts), rownames(res4$contrasts))
 
 # number of genes with significant post-transcriptional regulation
 sum(res3$tab.ExIn$FDR < 0.05)
@@ -678,7 +680,7 @@ 
    Calculate
 
    
 
    Statistical analysis
 
    
-
    Finally, we use the replicate measurement in the edgeR
+
    Finally, we use the replicate measurement in the edgeR
 framework to calculate the significance of the changes:
    
 
     # create DGEList object with exonic and intronic counts
@@ -779,13 +781,13 @@ 
    Session information
     sessionInfo()
-#> R version 4.4.1 (2024-06-14)
-#> Platform: x86_64-apple-darwin20
-#> Running under: macOS Monterey 12.7.6
+#> R Under development (unstable) (2025-01-03 r87521)
+#> Platform: aarch64-apple-darwin20
+#> Running under: macOS Sonoma 14.7.2
 #> 
 #> Matrix products: default
-#> BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
-#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
+#> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
+#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
 #> 
 #> locale:
 #> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
@@ -798,66 +800,65 @@ 
    Session information#> [8] methods   base     
 #> 
 #> other attached packages:
-#>  [1] edgeR_4.3.21           limma_3.61.12          QuasR_1.45.2          
-#>  [4] Rbowtie_1.45.0         rtracklayer_1.65.0     GenomicFeatures_1.57.1
-#>  [7] AnnotationDbi_1.67.0   Biobase_2.65.1         GenomicRanges_1.57.2  
-#> [10] GenomeInfoDb_1.41.2    IRanges_2.39.2         S4Vectors_0.43.2      
-#> [13] BiocGenerics_0.51.3    eisaR_1.19.0           BiocStyle_2.33.1      
+#>  [1] edgeR_4.5.1            limma_3.63.2           QuasR_1.47.2          
+#>  [4] Rbowtie_1.47.0         rtracklayer_1.67.0     GenomicFeatures_1.59.1
+#>  [7] AnnotationDbi_1.69.0   Biobase_2.67.0         GenomicRanges_1.59.1  
+#> [10] GenomeInfoDb_1.43.2    IRanges_2.41.2         S4Vectors_0.45.2      
+#> [13] BiocGenerics_0.53.3    generics_0.1.3         eisaR_1.19.0          
+#> [16] BiocStyle_2.35.0      
 #> 
 #> loaded via a namespace (and not attached):
 #>   [1] DBI_1.2.3                   bitops_1.0-9               
-#>   [3] deldir_2.0-4                httr2_1.0.5                
-#>   [5] biomaRt_2.61.3              rlang_1.1.4                
-#>   [7] magrittr_2.0.3              Rhisat2_1.21.0             
-#>   [9] matrixStats_1.4.1           compiler_4.4.1             
-#>  [11] RSQLite_2.3.7               png_0.1-8                  
+#>   [3] deldir_2.0-4                httr2_1.0.7                
+#>   [5] biomaRt_2.63.0              rlang_1.1.4                
+#>   [7] magrittr_2.0.3              Rhisat2_1.23.0             
+#>   [9] matrixStats_1.4.1           compiler_4.5.0             
+#>  [11] RSQLite_2.3.9               png_0.1-8                  
 #>  [13] systemfonts_1.1.0           vctrs_0.6.5                
-#>  [15] txdbmaker_1.1.2             stringr_1.5.1              
-#>  [17] pwalign_1.1.0               pkgconfig_2.0.3            
+#>  [15] txdbmaker_1.3.1             stringr_1.5.1              
+#>  [17] pwalign_1.3.1               pkgconfig_2.0.3            
 #>  [19] crayon_1.5.3                fastmap_1.2.0              
-#>  [21] dbplyr_2.5.0                XVector_0.45.0             
-#>  [23] utf8_1.2.4                  Rsamtools_2.21.2           
-#>  [25] rmarkdown_2.28              UCSC.utils_1.1.0           
-#>  [27] ragg_1.3.3                  bit_4.5.0                  
-#>  [29] xfun_0.48                   zlibbioc_1.51.2            
-#>  [31] cachem_1.1.0                jsonlite_1.8.9             
-#>  [33] progress_1.2.3              blob_1.2.4                 
-#>  [35] highr_0.11                  DelayedArray_0.31.14       
-#>  [37] BiocParallel_1.39.0         jpeg_0.1-10                
-#>  [39] prettyunits_1.2.0           R6_2.5.1                   
-#>  [41] VariantAnnotation_1.51.2    bslib_0.8.0                
-#>  [43] stringi_1.8.4               RColorBrewer_1.1-3         
-#>  [45] jquerylib_0.1.4             Rcpp_1.0.13                
-#>  [47] bookdown_0.41               SummarizedExperiment_1.35.5
-#>  [49] knitr_1.48                  SGSeq_1.39.0               
-#>  [51] igraph_2.1.1                tidyselect_1.2.1           
-#>  [53] Matrix_1.7-1                abind_1.4-8                
-#>  [55] yaml_2.3.10                 codetools_0.2-20           
-#>  [57] RUnit_0.4.33                hwriter_1.3.2.1            
-#>  [59] curl_5.2.3                  tibble_3.2.1               
-#>  [61] lattice_0.22-6              ShortRead_1.63.2           
-#>  [63] KEGGREST_1.45.1             evaluate_1.0.1             
-#>  [65] desc_1.4.3                  BiocFileCache_2.13.2       
-#>  [67] xml2_1.3.6                  Biostrings_2.73.2          
-#>  [69] filelock_1.0.3              pillar_1.9.0               
-#>  [71] BiocManager_1.30.25         MatrixGenerics_1.17.1      
-#>  [73] generics_0.1.3              RCurl_1.98-1.16            
-#>  [75] hms_1.1.3                   GenomicFiles_1.41.0        
-#>  [77] glue_1.8.0                  tools_4.4.1                
-#>  [79] interp_1.1-6                BiocIO_1.15.2              
-#>  [81] BSgenome_1.73.1             locfit_1.5-9.10            
-#>  [83] GenomicAlignments_1.41.0    fs_1.6.4                   
-#>  [85] XML_3.99-0.17               grid_4.4.1                 
-#>  [87] latticeExtra_0.6-30         GenomeInfoDbData_1.2.13    
-#>  [89] restfulr_0.0.15             cli_3.6.3                  
-#>  [91] rappdirs_0.3.3              textshaping_0.4.0          
-#>  [93] fansi_1.0.6                 S4Arrays_1.5.11            
-#>  [95] dplyr_1.1.4                 sass_0.4.9                 
-#>  [97] digest_0.6.37               SparseArray_1.5.45         
-#>  [99] rjson_0.2.23                memoise_2.0.1              
-#> [101] htmltools_0.5.8.1           pkgdown_2.1.1.9000         
-#> [103] lifecycle_1.0.4             httr_1.4.7                 
-#> [105] statmod_1.5.0               bit64_4.5.2
    
+#>  [21] dbplyr_2.5.0                XVector_0.47.1             
+#>  [23] Rsamtools_2.23.1            rmarkdown_2.29             
+#>  [25] UCSC.utils_1.3.0            ragg_1.3.3                 
+#>  [27] bit_4.5.0.1                 xfun_0.49                  
+#>  [29] zlibbioc_1.53.0             cachem_1.1.0               
+#>  [31] jsonlite_1.8.9              progress_1.2.3             
+#>  [33] blob_1.2.4                  DelayedArray_0.33.3        
+#>  [35] BiocParallel_1.41.0         jpeg_0.1-10                
+#>  [37] prettyunits_1.2.0           R6_2.5.1                   
+#>  [39] VariantAnnotation_1.53.0    bslib_0.8.0                
+#>  [41] stringi_1.8.4               RColorBrewer_1.1-3         
+#>  [43] jquerylib_0.1.4             Rcpp_1.0.13-1              
+#>  [45] bookdown_0.41               SummarizedExperiment_1.37.0
+#>  [47] knitr_1.49                  SGSeq_1.41.0               
+#>  [49] igraph_2.1.2                tidyselect_1.2.1           
+#>  [51] Matrix_1.7-1                abind_1.4-8                
+#>  [53] yaml_2.3.10                 codetools_0.2-20           
+#>  [55] RUnit_0.4.33                hwriter_1.3.2.1            
+#>  [57] curl_6.0.1                  tibble_3.2.1               
+#>  [59] lattice_0.22-6              ShortRead_1.65.0           
+#>  [61] KEGGREST_1.47.0             evaluate_1.0.1             
+#>  [63] desc_1.4.3                  BiocFileCache_2.15.0       
+#>  [65] xml2_1.3.6                  Biostrings_2.75.3          
+#>  [67] filelock_1.0.3              pillar_1.10.0              
+#>  [69] BiocManager_1.30.25         MatrixGenerics_1.19.0      
+#>  [71] RCurl_1.98-1.16             hms_1.1.3                  
+#>  [73] GenomicFiles_1.43.0         glue_1.8.0                 
+#>  [75] tools_4.5.0                 interp_1.1-6               
+#>  [77] BiocIO_1.17.1               BSgenome_1.75.0            
+#>  [79] locfit_1.5-9.10             GenomicAlignments_1.43.0   
+#>  [81] fs_1.6.5                    XML_3.99-0.18              
+#>  [83] grid_4.5.0                  latticeExtra_0.6-30        
+#>  [85] GenomeInfoDbData_1.2.13     restfulr_0.0.15            
+#>  [87] cli_3.6.3                   rappdirs_0.3.3             
+#>  [89] textshaping_0.4.1           S4Arrays_1.7.1             
+#>  [91] dplyr_1.1.4                 sass_0.4.9                 
+#>  [93] digest_0.6.37               SparseArray_1.7.2          
+#>  [95] rjson_0.2.23                memoise_2.0.1              
+#>  [97] htmltools_0.5.8.1           pkgdown_2.1.1.9000         
+#>  [99] lifecycle_1.0.4             httr_1.4.7                 
+#> [101] statmod_1.5.0               bit64_4.5.2

    References diff --git a/articles/rna-velocity.html b/articles/rna-velocity.html index 1e0c01e..a1b068a 100644 --- a/articles/rna-velocity.html +++ b/articles/rna-velocity.html @@ -88,7 +88,7 @@

    Generating reference files for spliced and

    Charlotte Soneson

    -

    2024-10-29

    +

    2025-01-06

    Source: vignettes/rna-velocity.Rmd @@ -121,7 +121,7 @@

    Generate feature rangesGencode release 28. We extract genomic ranges for spliced transcript and introns, where the latter are defined for each transcript separately -(using the same terminology as in the BUSpaRse +(using the same terminology as in the BUSpaRse package). For each intron, a flanking sequence of 50 nt is added on each side to accommodate reads mapping across an exon/intron boundary.

    @@ -135,11 +135,15 @@ 
    Generate feature ranges  joinOverlappingIntrons = FALSE, 
   verbose = TRUE
 )
+#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
+#>   object 'type_sum.accel' not found
 #> Import genomic features from the file as a GRanges object ... OK
 #> Prepare the 'metadata' data frame ... OK
 #> Make the TxDb object ...
-#> Warning in .get_cds_IDX(mcols0$type, mcols0$phase): The "phase" metadata column contains non-NA values for
-#>   features of type stop_codon. This information was ignored.
+#> Warning in .get_cds_IDX(mcols0$type, mcols0$phase): The "phase" metadata column contains non-NA values for features of
+#>   type stop_codon. This information was ignored.
+#> Warning in .makeTxDb_normarg_chrominfo(chrominfo): genome version
+#> information is not available for this TxDb object
 #> OK
 #> 'select()' returned 1:1 mapping between keys and columns
 #> Extracting spliced transcript features
@@ -243,7 +247,7 @@ 
    Extract feature sequences
 
    Once the genomic ranges of the features of interest are extracted, we
 can obtain the nucleotide sequences using the
-extractTranscriptSeqs() function from the GenomicFeatures
+extractTranscriptSeqs() function from the GenomicFeatures
 package. In addition to the ranges, this requires the genome sequence.
 This can be obtained, for example, from the corresponding BSgenome
 package, or from an external FASTA file.
    
@@ -280,7 +284,7 @@ 
    Generate an expanded GTF filetximeta.
    
+abundances with tximeta.
    
 
     exportToGtf(
   grl, 
@@ -323,13 +327,13 @@ 
    Session info
     sessionInfo()
-#> R version 4.4.1 (2024-06-14)
-#> Platform: x86_64-apple-darwin20
-#> Running under: macOS Monterey 12.7.6
+#> R Under development (unstable) (2025-01-03 r87521)
+#> Platform: aarch64-apple-darwin20
+#> Running under: macOS Sonoma 14.7.2
 #> 
 #> Matrix products: default
-#> BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
-#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
+#> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
+#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
 #> 
 #> locale:
 #> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
@@ -343,66 +347,66 @@ 
    Session info#> 
 #> other attached packages:
 #>  [1] BSgenome.Hsapiens.UCSC.hg38_1.4.5
-#>  [2] BSgenome_1.73.1                  
-#>  [3] rtracklayer_1.65.0               
-#>  [4] BiocIO_1.15.2                    
-#>  [5] Biostrings_2.73.2                
-#>  [6] XVector_0.45.0                   
-#>  [7] GenomicRanges_1.57.2             
-#>  [8] GenomeInfoDb_1.41.2              
-#>  [9] IRanges_2.39.2                   
-#> [10] S4Vectors_0.43.2                 
-#> [11] BiocGenerics_0.51.3              
-#> [12] eisaR_1.19.0                     
-#> [13] BiocStyle_2.33.1                 
+#>  [2] BSgenome_1.75.0                  
+#>  [3] rtracklayer_1.67.0               
+#>  [4] BiocIO_1.17.1                    
+#>  [5] Biostrings_2.75.3                
+#>  [6] XVector_0.47.1                   
+#>  [7] GenomicRanges_1.59.1             
+#>  [8] GenomeInfoDb_1.43.2              
+#>  [9] IRanges_2.41.2                   
+#> [10] S4Vectors_0.45.2                 
+#> [11] BiocGenerics_0.53.3              
+#> [12] generics_0.1.3                   
+#> [13] eisaR_1.19.0                     
+#> [14] BiocStyle_2.35.0                 
 #> 
 #> loaded via a namespace (and not attached):
 #>  [1] tidyselect_1.2.1            dplyr_1.1.4                
 #>  [3] blob_1.2.4                  filelock_1.0.3             
 #>  [5] bitops_1.0-9                fastmap_1.2.0              
-#>  [7] RCurl_1.98-1.16             BiocFileCache_2.13.2       
-#>  [9] GenomicAlignments_1.41.0    XML_3.99-0.17              
+#>  [7] RCurl_1.98-1.16             BiocFileCache_2.15.0       
+#>  [9] GenomicAlignments_1.43.0    XML_3.99-0.18              
 #> [11] digest_0.6.37               lifecycle_1.0.4            
-#> [13] statmod_1.5.0               KEGGREST_1.45.1            
-#> [15] RSQLite_2.3.7               magrittr_2.0.3             
-#> [17] compiler_4.4.1              rlang_1.1.4                
+#> [13] statmod_1.5.0               KEGGREST_1.47.0            
+#> [15] RSQLite_2.3.9               magrittr_2.0.3             
+#> [17] compiler_4.5.0              rlang_1.1.4                
 #> [19] sass_0.4.9                  progress_1.2.3             
-#> [21] tools_4.4.1                 utf8_1.2.4                 
-#> [23] yaml_2.3.10                 knitr_1.48                 
-#> [25] prettyunits_1.2.0           S4Arrays_1.5.11            
-#> [27] bit_4.5.0                   curl_5.2.3                 
-#> [29] DelayedArray_0.31.14        xml2_1.3.6                 
-#> [31] abind_1.4-8                 BiocParallel_1.39.0        
-#> [33] txdbmaker_1.1.2             desc_1.4.3                 
-#> [35] grid_4.4.1                  fansi_1.0.6                
-#> [37] edgeR_4.3.21                biomaRt_2.61.3             
-#> [39] SummarizedExperiment_1.35.5 cli_3.6.3                  
-#> [41] rmarkdown_2.28              crayon_1.5.3               
-#> [43] generics_0.1.3              ragg_1.3.3                 
-#> [45] httr_1.4.7                  rjson_0.2.23               
-#> [47] DBI_1.2.3                   cachem_1.1.0               
-#> [49] stringr_1.5.1               zlibbioc_1.51.2            
-#> [51] parallel_4.4.1              AnnotationDbi_1.67.0       
-#> [53] BiocManager_1.30.25         restfulr_0.0.15            
-#> [55] matrixStats_1.4.1           vctrs_0.6.5                
-#> [57] Matrix_1.7-1                jsonlite_1.8.9             
-#> [59] bookdown_0.41               hms_1.1.3                  
-#> [61] bit64_4.5.2                 systemfonts_1.1.0          
-#> [63] GenomicFeatures_1.57.1      locfit_1.5-9.10            
-#> [65] limma_3.61.12               jquerylib_0.1.4            
-#> [67] glue_1.8.0                  pkgdown_2.1.1.9000         
-#> [69] codetools_0.2-20            stringi_1.8.4              
-#> [71] UCSC.utils_1.1.0            tibble_3.2.1               
-#> [73] pillar_1.9.0                rappdirs_0.3.3             
-#> [75] htmltools_0.5.8.1           GenomeInfoDbData_1.2.13    
-#> [77] dbplyr_2.5.0                httr2_1.0.5                
-#> [79] R6_2.5.1                    textshaping_0.4.0          
-#> [81] evaluate_1.0.1              lattice_0.22-6             
-#> [83] Biobase_2.65.1              png_0.1-8                  
-#> [85] Rsamtools_2.21.2            memoise_2.0.1              
-#> [87] bslib_0.8.0                 SparseArray_1.5.45         
-#> [89] xfun_0.48                   fs_1.6.4                   
-#> [91] MatrixGenerics_1.17.1       pkgconfig_2.0.3
    
+#> [21] tools_4.5.0                 yaml_2.3.10                
+#> [23] knitr_1.49                  prettyunits_1.2.0          
+#> [25] S4Arrays_1.7.1              bit_4.5.0.1                
+#> [27] curl_6.0.1                  DelayedArray_0.33.3        
+#> [29] xml2_1.3.6                  abind_1.4-8                
+#> [31] BiocParallel_1.41.0         txdbmaker_1.3.1            
+#> [33] desc_1.4.3                  grid_4.5.0                 
+#> [35] edgeR_4.5.1                 biomaRt_2.63.0             
+#> [37] SummarizedExperiment_1.37.0 cli_3.6.3                  
+#> [39] rmarkdown_2.29              crayon_1.5.3               
+#> [41] ragg_1.3.3                  httr_1.4.7                 
+#> [43] rjson_0.2.23                DBI_1.2.3                  
+#> [45] cachem_1.1.0                stringr_1.5.1              
+#> [47] zlibbioc_1.53.0             parallel_4.5.0             
+#> [49] AnnotationDbi_1.69.0        BiocManager_1.30.25        
+#> [51] restfulr_0.0.15             matrixStats_1.4.1          
+#> [53] vctrs_0.6.5                 Matrix_1.7-1               
+#> [55] jsonlite_1.8.9              bookdown_0.41              
+#> [57] hms_1.1.3                   bit64_4.5.2                
+#> [59] systemfonts_1.1.0           GenomicFeatures_1.59.1     
+#> [61] locfit_1.5-9.10             limma_3.63.2               
+#> [63] jquerylib_0.1.4             glue_1.8.0                 
+#> [65] pkgdown_2.1.1.9000          codetools_0.2-20           
+#> [67] stringi_1.8.4               UCSC.utils_1.3.0           
+#> [69] tibble_3.2.1                pillar_1.10.0              
+#> [71] rappdirs_0.3.3              htmltools_0.5.8.1          
+#> [73] GenomeInfoDbData_1.2.13     dbplyr_2.5.0               
+#> [75] httr2_1.0.7                 R6_2.5.1                   
+#> [77] textshaping_0.4.1           evaluate_1.0.1             
+#> [79] lattice_0.22-6              Biobase_2.67.0             
+#> [81] png_0.1-8                   Rsamtools_2.23.1           
+#> [83] memoise_2.0.1               bslib_0.8.0                
+#> [85] SparseArray_1.7.2           xfun_0.49                  
+#> [87] fs_1.6.5                    MatrixGenerics_1.19.0      
+#> [89] pkgconfig_2.0.3

    diff --git a/pkgdown.yml b/pkgdown.yml index 4a3d203..bb1c1f8 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,10 +1,10 @@ pandoc: 3.1.11 pkgdown: 2.1.1.9000 -pkgdown_sha: ffe60d5f60934e95285d416dae12c05e24ed1dac +pkgdown_sha: 4519ca0ae415b415eb8c1c142a6d4d39d8a5b80d articles: eisaR: eisaR.html rna-velocity: rna-velocity.html -last_built: 2024-10-29T17:26Z +last_built: 2025-01-06T12:49Z urls: reference: https://fmicompbio.github.io/eisaR/reference article: https://fmicompbio.github.io/eisaR/articles diff --git a/reference/exportToGtf.html b/reference/exportToGtf.html index bcbf17e..074959f 100644 --- a/reference/exportToGtf.html +++ b/reference/exportToGtf.html @@ -118,6 +118,7 @@

    Examples

    #> Prepare the 'metadata' data frame ... #> OK #> Make the TxDb object ... +#> Warning: genome version information is not available for this TxDb object #> OK #> 'select()' returned 1:1 mapping between keys and columns #> Extracting spliced transcript features diff --git a/reference/getFeatureRanges.html b/reference/getFeatureRanges.html index a56f76f..3ea3066 100644 --- a/reference/getFeatureRanges.html +++ b/reference/getFeatureRanges.html @@ -161,6 +161,7 @@

    Examples

    #> Prepare the 'metadata' data frame ... #> OK #> Make the TxDb object ... +#> Warning: genome version information is not available for this TxDb object #> OK #> 'select()' returned 1:1 mapping between keys and columns #> Extracting spliced transcript features @@ -250,6 +251,13 @@

    Examples

    seqs } #> Loading required package: BiocGenerics +#> Loading required package: generics +#> +#> Attaching package: ‘generics’ +#> The following objects are masked from ‘package:base’: +#> +#> as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, +#> setequal, union #> #> Attaching package: ‘BiocGenerics’ #> The following objects are masked from ‘package:stats’: @@ -259,10 +267,10 @@

    Examples

    #> #> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, #> as.data.frame, basename, cbind, colnames, dirname, do.call, -#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, -#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, -#> pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, -#> tapply, union, unique, unsplit, which.max, which.min +#> duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, +#> mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, +#> rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, +#> unsplit, which.max, which.min #> Loading required package: S4Vectors #> Loading required package: stats4 #> diff --git a/reference/getTx2Gene.html b/reference/getTx2Gene.html index d474474..b38a15c 100644 --- a/reference/getTx2Gene.html +++ b/reference/getTx2Gene.html @@ -114,6 +114,7 @@

    Examples

    #> Prepare the 'metadata' data frame ... #> OK #> Make the TxDb object ... +#> Warning: genome version information is not available for this TxDb object #> OK #> 'select()' returned 1:1 mapping between keys and columns #> Extracting spliced transcript features