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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
library("BiocStyle")
```
# recount3 <img src="man/figures/logo.png" align="right" width="200px" >
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/recount3)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/recount3)
[](http://bioconductor.org/packages/stats/bioc/recount3/)
[](https://support.bioconductor.org/tag/recount3)
[](https://bioconductor.org/packages/release/bioc/html/recount3.html#since)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/recount3/)
[](https://bioconductor.org/packages/release/bioc/html/recount3.html#since)
[](https://codecov.io/gh/LieberInstitute/recount3?branch=master)
[](https://github.com/LieberInstitute/recount3/actions/workflows/check-bioc.yml)
[](https://github.com/LieberInstitute/recount3/issues)
[](https://github.com/LieberInstitute/recount3/pulls)
<!-- badges: end -->
The `r Biocpkg('recount3')` R/Bioconductor package is part of the `recount3` project and is the latest iteration of the `ReCount` family of projects that provide access to uniformly-processed RNA sequencing datasets. The **main documentation website** for all the `recount3`-related projects is available at [**recount.bio**](https://LieberInstitute.github.io/recount3-docs). Please check that website for more information about how this R/Bioconductor package and other tools are related to each other.
## Documentation
For more information about `r Biocpkg('recount3')` check the vignettes [through Bioconductor](http://bioconductor.org/packages/recount3) or at the [documentation website](http://lieberinstitute.github.io/recount3).
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `r Biocpkg('recount3')` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("recount3")
```
## Citation
Below is the citation output from using `citation('recount3')` in R. Please
run this yourself to check for any updates on how to cite __recount3__.
```{r 'citation', eval = requireNamespace('recount3')}
print(citation("recount3"), bibtex = TRUE)
```
Please note that `r Biocpkg('recount3')` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
## Code of Conduct
Please note that the derfinderPlot project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
## Development tools
* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, `r BiocStyle::Githubpkg('r-hub/sysreqs')` and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://lieberinstitute.github.io/recount3) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
For more details, check the `dev` directory.
## Project history
To clarify the relationship between the R/Bioconductor packages and the phases of `ReCount` please check the table below:
| Year | Phase | Main references | R/Bioconductor |
| --- | --- | --- | --- |
| 2011 | [`ReCount`](http://bowtie-bio.sourceforge.net/recount/) | DOI: [10.1186/1471-2105-12-449](https://doi.org/10.1186/1471-2105-12-449) | none |
| 2017 | [`recount2`](https://jhubiostatistics.shinyapps.io/recount/) | DOI: [10.1038/nbt.3838](https://doi.org/10.1038/nbt.3838) [10.12688/f1000research.12223.1](https://doi.org/10.12688/f1000research.12223.1) | `r Biocpkg('recount')` |
| 2021 | [`recount3`](https://LieberInstitute.github.io/recount3-docs) | DOI: [10.1186/s13059-021-02533-6](https://doi.org/10.1186/s13059-021-02533-6) | `r Biocpkg('recount3')` |
## Teams involved
The `ReCount` family involves the following teams:
* [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/)
* [Leonardo Collado-Torres](http://lcolladotor.github.io/) and [Andrew E. Jaffe](http://aejaffe.com/) from [LIBD](https://www.libd.org/)
* [Abhinav Nellore's lab at OHSU](http://nellore.bio/)
* [Jeff Leek's lab at JHBSPH Biostatistics Deparment](http://jtleek.com/)
* Data hosted by the [Registry of Open Data on AWS](https://registry.opendata.aws/recount/) and [SciServer from IDIES at JHU](https://www.sciserver.org/) through a load balancer called [duffel](https://github.com/nellore/digitalocean-duffel).
| | | | | |
| --- | --- | --- | --- | --- |
| <a href="http://www.langmead-lab.org/"><img src="http://www.langmead-lab.org/wp-content/uploads/2014/01/Screen-Shot-2014-02-02-at-5.20.13-PM-1024x199.png" width="250px"></a> | <a href="https://www.libd.org/"><img src="http://lcolladotor.github.io/img/LIBD_logo.jpg" width="250px"></a> | <a href="http://nellore.bio/"><img src="https://seekvectorlogo.net/wp-content/uploads/2018/08/oregon-health-science-university-ohsu-vector-logo.png" width="250px"></a> | <a href="https://www.sciserver.org/"><img src="https://skyserver.sdss.org/dr14/en/images/sciserver_logo_inverted_vertical.png" width="250px"></a> | <a href="https://registry.opendata.aws/recount/"><img src="https://assets.opendata.aws/img/AWS-Logo_White-Color_300x180.png" width="250px"></a> |
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