recount3

Explore and download data from the recount3 project

https://github.com/lieberinstitute/recount3

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Explore and download data from the recount3 project

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
library("BiocStyle")
```

# recount3 


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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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