Re-organize a bit: add PARTs, add a new chapter, start some of the data chapter

Author: lcolladotor

01_data.Rmd

@@ -0,0 +1,22 @@
+# (PART) Get RNA-seq data! {-}
+
+# Data
+
+`recount3` provides processed RNA-seq data for human and mouse in file formats similar to `recount2` (Figure \@ref(fig:recountWorkflowFig1)), which at its core is based on coverage bigWig files and exon-exon junction counts (see [Raw file](#raw-files) for more details). These two raw files power the whole `recount3` ecosystem. In `recount3`, we have provided coverage count files for several human and mouse annotations with samples grouped by study. Some large studies, like [GTEx](TODO) and [TCGA](TODO) have been fragmented at the tissue level to make the data more accessible.
+
+```{r "recountWorkflowFig1", out.width="100%", fig.align="center", fig.cap = "Overview of the data available in recount2 and recount3. Reads (pink boxes) aligned to the reference genome can be used to compute a base-pair coverage curve and identify exon-exon junctions (split reads). Gene and exon count matrices are generated using annotation information providing the gene (green boxes) and exon (blue boxes) coordinates together with the base-level coverage curve. The reads spanning exon-exon junctions (jx) are used to compute a third count matrix that might include unannotated junctions (jx 3 and 4). Without using annotation information, expressed regions (orange box) can be determined from the base-level coverage curve to then construct data-driven count matrices.", echo = FALSE}
+knitr::include_graphics("images/recountWorkflow_Figure1.png")
+```
+
+## Human
+
+Annotations:
+
+* Gencode v26
+* Gencode v29
+* RefSeq
+* FANTOM6_cat
+* ERCC
+* SIRV
+
+## Mouse

02_data.Rmd

@@ -0,0 +1,3 @@
+# Study explorer
+
+We can embed `shiny` web applications here

03_quick_access.Rmd 02_quick_access.Rmd

@@ -0,0 +1,4 @@
+# (PART) Details {-}
+
+# Quality check fields
+

03_explore.Rmd

@@ -0,0 +1,5 @@
+# Raw files
+
+Explain the raw file formats we have and how they are organized
+
+## Data source vs collection

04_explore.Rmd

@@ -0,0 +1,13 @@
+# (PART) Expand `ReCount` {-}
+
+# Your data
+
+## Process your data
+
+Info on how to use `recount-pump` for your own data
+
+
+## Contribute your collections
+
+How to build a collection and send that information to us
+

04_qc.Rmd

@@ -1 +1,12 @@
-# Join the `ReCount` team!
+# Join the `ReCount` team!
+
+We have multiple **positions available**! The `ReCount` project involves the Hansen, Leek, Langmead and Battle labs at JHU & the Nellore lab at OHSU & the Collado-Torres lab at LIBD.
+
+Contact: 
+
+* [Kasper D. Hansen](www.hansenlab.org)
+* [Ben Langmead](www.langmead-lab.org/)
+* [Leonardo Collado-Torres](https://lcolladotor.github.io/)
+* [Abhinav Nellore](nellore.bio/)
+* [Alexis Battle](battlelab.jhu.edu/)
+* [Jeff Leek](jtleek.com/)

06_bioconductor.Rmd 05_bioconductor.Rmd

@@ -7,7 +7,7 @@ output:
   bookdown::gitbook: default
 ---
 
-# Overview
+# Overview {-}
 
 Welcome to the home of the `recount3` project! This website is the home to the most updated version of all the documentation related to the `recount3` project.
 
@@ -17,52 +17,52 @@ The raw sequencing data were processed with [`recount-pump`](https://github.com/
 
 By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.
 
+## Related `recount3` websites {-}
 
-## How to cite `recount3`
+`recount3` is composed of several related software tools and websites. Here is the full list, with all of them referring to this website for their unified documentation.
+
+* [`recount-pump`](https://github.com/langmead-lab/recount-pump/): TODO 
+* `recount-unifier`: TODO
+* `monorail`: TODO
+* `megadepth`: TODO
+* `recount3`: R package [source](https://github.com/LieberInstitute/recount3), Bioconductor [landing page](https://bioconductor.org/packages/recount3), `pkgdown` documentation [website](https://LieberInstitute.github.io/recount3)
+* [`recount3-docs`](https://github.com/LieberInstitute/recount3-docs): the source code for this documentation [website](https://LieberInstitute.github.io/recount3-docs).
+
+
+
+## How to cite `recount3` {-}
 
 Thank you for your continued support of the `ReCount` family of projects! We greatly appreciate you citing our work.
 
-```{r}
+```{r "citation"}
 print(citation("recount3")[2], bibtex = TRUE)
 ```
 
-### Related projects
+### Related projects {-}
 
 The `ReCount` project has three main publications over the years with implementation details that have been improved each time. Each phase of the project has had several companion publications that expanded the main resource in different directions. Please cite the appropriate expansions and results as you see relevant for your work.
 
-### Previous `ReCount` projects
+### Previous `ReCount` projects {-}
 
 * [`recount2`](https://jhubiostatistics.shinyapps.io/recount/)
 * [`ReCount`](http://bowtie-bio.sourceforge.net/recount/)
 
-### Related publications
+### Related publications {-}
 
-#### `recount3`
+#### `recount3` {-}
 
-#### `recount2`
+#### `recount2` {-}
 
-#### `ReCount`
+#### `ReCount` {-}
 
-## Related `recount3` websites
-
-`recount3` is composed of several related software tools and websites. Here is the full list, with all of them referring to this website for their unified documentation.
-
-* [`recount-pump`](https://github.com/langmead-lab/recount-pump/): TODO 
-* `recount-unifier`: TODO
-* `monorail`: TODO
-* `megadepth`: TODO
-* `recount3`: R package [source](https://github.com/LieberInstitute/recount3), Bioconductor [landing page](https://bioconductor.org/packages/recount3), `pkgdown` documentation [website](https://LieberInstitute.github.io/recount3)
-* [`recount3-docs`]((https://github.com/LieberInstitute/recount3-docs): the source code for this documentation [website](https://LieberInstitute.github.io/recount3-docs).
-
-
-## Team members
+## Team members {-}
 
 * [Christopher Wilks](https://github.com/) (the star behind `recount3`!)
 * [Leonardo Collado Torres](https://github.com/lcolladotor) 
 * [Shijie Charles Zheng](https://github.com/)
 
 
-## Teams involved
+## Teams involved {-}
 
 * [Ben Langmead's lab at JHU Computer Science](http://www.langmead-lab.org/)
 * [Kasper Daniel Hansen's lab at JHBSPH Biostatistics Department](https://www.hansenlab.org/)
@@ -76,3 +76,23 @@ The `ReCount` project has three main publications over the years with implementa
 
 
 This book was last updated on `r Sys.time()`.
+
+## R session information {-}
+
+Details on the R version used for making this book. The source code is available at [`lcolladotor/bioc_team_ds`](https://github.com/lcolladotor/bioc_team_ds).
+
+```{r session_info_chunk, eval = FALSE}
+## Load the package at the top of your script
+library("sessioninfo")
+
+## Reproducibility information
+print('Reproducibility information:')
+Sys.time()
+proc.time()
+options(width = 120)
+session_info()
+```
+
+```{r session_info, echo = FALSE}
+<<session_info_chunk>>
+```