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https://github.com/lieberinstitute/recount3

Explore and download data from the recount3 project
https://github.com/lieberinstitute/recount3

annotation-agnostic bioconductor count derfinder exon gene human illumina junction mouse r recount recount3 rnaseq rstats

Last synced: 7 days ago
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Explore and download data from the recount3 project

Host: GitHub
URL: https://github.com/lieberinstitute/recount3
Owner: LieberInstitute
Created: 2020-04-14T14:20:00.000Z (almost 5 years ago)
Default Branch: devel
Last Pushed: 2024-12-10T22:03:21.000Z (about 2 months ago)
Last Synced: 2025-01-14T00:10:19.342Z (14 days ago)
Topics: annotation-agnostic, bioconductor, count, derfinder, exon, gene, human, illumina, junction, mouse, r, recount, recount3, rnaseq, rstats
Language: R
Homepage: http://lieberinstitute.github.io/recount3
Size: 2.87 MB
Stars: 31
Watchers: 8
Forks: 4
Open Issues: 20
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Support: .github/SUPPORT.md

Awesome Lists containing this project

README

        ---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

    collapse = TRUE,

    comment = "#>",

    fig.path = "man/figures/README-",

    out.width = "100%"

)

library("BiocStyle")

```

# recount3 

[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)

[![Bioc release status](http://www.bioconductor.org/shields/build/release/bioc/recount3.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/recount3)

[![Bioc devel status](http://www.bioconductor.org/shields/build/devel/bioc/recount3.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/recount3)

[![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/recount3.svg)](http://bioconductor.org/packages/stats/bioc/recount3/)

[![Bioc support](https://bioconductor.org/shields/posts/recount3.svg)](https://support.bioconductor.org/tag/recount3)

[![Bioc history](https://bioconductor.org/shields/years-in-bioc/recount3.svg)](https://bioconductor.org/packages/release/bioc/html/recount3.html#since)

[![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/bioc/recount3.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/recount3/)

[![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/recount3.svg)](https://bioconductor.org/packages/release/bioc/html/recount3.html#since)

[![Codecov test coverage](https://codecov.io/gh/LieberInstitute/recount3/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/recount3?branch=master)

[![R build status](https://github.com/LieberInstitute/recount3/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/recount3/actions/workflows/check-bioc.yml)

[![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/recount3)](https://github.com/LieberInstitute/recount3/issues)

[![GitHub pulls](https://img.shields.io/github/issues-pr/LieberInstitute/recount3)](https://github.com/LieberInstitute/recount3/pulls)

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).

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