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README.Rmd
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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%"
)
```
# recount <img src="man/figures/logo.png" align="right" width="400px" />
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/recount)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/recount)
[](http://bioconductor.org/packages/stats/bioc/recount/)
[](https://support.bioconductor.org/tag/recount)
[](https://bioconductor.org/packages/release/bioc/html/recount.html#since)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/recount/)
[](https://bioconductor.org/packages/release/bioc/html/recount.html#since)
[](https://codecov.io/gh/leekgroup/recount?branch=devel)
[](https://github.com/leekgroup/recount/actions)
[](https://github.com/leekgroup/recount/issues)
[](https://github.com/leekgroup/recount/pulls)
<!-- badges: end -->
Explore and download data from the recount project available at the [recount2 website](https://jhubiostatistics.shinyapps.io/recount/). Using the `recount` package you can download _RangedSummarizedExperiment_ objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The _RangedSummarizedExperiment_ objects can be used by different packages for performing differential expression analysis. Using [derfinder](http://bioconductor.org/packages/derfinder) you can perform annotation-agnostic differential expression analyses with the data from the recount project.
## Documentation
For more information about `recount` check the vignettes [through Bioconductor](http://bioconductor.org/packages/recount) or at the [documentation website](http://leekgroup.github.io/recount).
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `recount` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("recount")
```
## Citation
Below is the citation output from using `citation('recount')` in R. Please
run this yourself to check for any updates on how to cite __recount__.
```{r 'citation', eval = requireNamespace('recount')}
print(citation("recount"), bibtex = TRUE)
```
Please note that the `recount` 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 recount 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://leekgroup.github.io/recount) 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.
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.
## Teams involved
* [Jeff Leek's lab at JHBSPH Biostatistics Department](http://jtleek.com/),
* [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/),
* Data hosted by [SciServer at JHU](https://www.sciserver.org/).
| | | | |
| --- | --- | --- | --- |
| <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> |
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