<!-- README.md is generated from README.Rmd. Please edit that file --> # 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 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 print(citation("recount"), bibtex = TRUE) #> To cite package 'recount' in publications use: #> #> Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, #> Jaffe AE, Langmead B, Leek JT (2017). "Reproducible RNA-seq analysis #> using recount2." _Nature Biotechnology_. doi:10.1038/nbt.3838 #> <https://doi.org/10.1038/nbt.3838>, #> <http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html>. #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {Reproducible RNA-seq analysis using recount2}, #> author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E. Ellis and Margaret A. Taub and Kasper D. Hansen and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek}, #> year = {2017}, #> journal = {Nature Biotechnology}, #> doi = {10.1038/nbt.3838}, #> url = {http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html}, #> } #> #> Collado-Torres L, Nellore A, Jaffe AE (2017). "recount workflow: #> Accessing over 70,000 human RNA-seq samples with Bioconductor #> [version 1; referees: 1 approved, 2 approved with reservations]." #> _F1000Research_. doi:10.12688/f1000research.12223.1 #> <https://doi.org/10.12688/f1000research.12223.1>, #> <https://f1000research.com/articles/6-1558/v1>. #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]}, #> author = {Leonardo Collado-Torres and Abhinav Nellore and Andrew E. Jaffe}, #> year = {2017}, #> journal = {F1000Research}, #> doi = {10.12688/f1000research.12223.1}, #> url = {https://f1000research.com/articles/6-1558/v1}, #> } #> #> Ellis SE, Collado-Torres L, Jaffe AE, Leek JT (2018). "Improving the #> value of public RNA-seq expression data by phenotype prediction." #> _Nucl. Acids Res._. doi:10.1093/nar/gky102 #> <https://doi.org/10.1093/nar/gky102>, #> <https://doi.org/10.1093/nar/gky102>. #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {Improving the value of public RNA-seq expression data by phenotype prediction}, #> author = {Shannon E. Ellis and Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek}, #> year = {2018}, #> journal = {Nucl. Acids Res.}, #> doi = {10.1093/nar/gky102}, #> url = {https://doi.org/10.1093/nar/gky102}, #> } #> #> Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, #> Jaffe AE, Langmead B, Leek JT (2023). _Explore and download data from #> the recount project_. doi:10.18129/B9.bioc.recount #> <https://doi.org/10.18129/B9.bioc.recount>, #> https://github.com/leekgroup/recount - R package version 1.27.0, #> <http://www.bioconductor.org/packages/recount>. #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {Explore and download data from the recount project}, #> author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E. Ellis and Margaret A. Taub and Kasper D. Hansen and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek}, #> year = {2023}, #> url = {http://www.bioconductor.org/packages/recount}, #> note = {https://github.com/leekgroup/recount - R package version 1.27.0}, #> doi = {10.18129/B9.bioc.recount}, #> } #> #> Frazee AC, Langmead B, Leek JT (2011). "ReCount: A multi-experiment #> resource of analysis-ready RNA-seq gene count datasets." _BMC #> Bioinformatics_. doi:10.1186/1471-2105-12-449 #> <https://doi.org/10.1186/1471-2105-12-449>, #> <https://doi.org/10.1186/1471-2105-12-449>. #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets}, #> author = {Alyssa C. Frazee and Ben Langmead and Jeffrey T. Leek}, #> year = {2011}, #> journal = {BMC Bioinformatics}, #> doi = {10.1186/1471-2105-12-449}, #> url = {https://doi.org/10.1186/1471-2105-12-449}, #> } #> #> Razmara A, Ellis SE, Sokolowski DJ, Davis S, Wilson MD, Leek JT, #> Jaffe AE, Collado-Torres L (2019). "recount-brain: a curated #> repository of human brain RNA-seq datasets metadata." _bioRxiv_. #> doi:10.1101/618025 <https://doi.org/10.1101/618025>, #> <https://doi.org/10.1101/618025>. #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {recount-brain: a curated repository of human brain RNA-seq datasets metadata}, #> author = {Ashkaun Razmara and Shannon E. Ellis and Dustin J. Sokolowski and Sean Davis and Michael D. Wilson and Jeffrey T. Leek and Andrew E. Jaffe and Leonardo Collado-Torres}, #> year = {2019}, #> journal = {bioRxiv}, #> doi = {10.1101/618025}, #> url = {https://doi.org/10.1101/618025}, #> } #> #> Imada E, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara #> W, Stupnikov A, Lobo-Pereira F, Yip C, Yasuzawa K, Kondo N, Itoh M, #> Suzuki H, Kasukawa T, Hon CC, de Hoon MJ, Shin JW, Carninci P, Jaffe #> AE, Leek JT, Favorov A, Franco GR, Langmead B, Marchionni L (2020). #> "Recounting the FANTOM CAGE–Associated Transcriptome." _Genome #> Research_. doi:10.1101/gr.254656.119 #> <https://doi.org/10.1101/gr.254656.119>, #> <https://doi.org/10.1101/gr.254656.119>. #> #> A BibTeX entry for LaTeX users is #> #> @Article{, #> title = {Recounting the FANTOM CAGE–Associated Transcriptome}, #> author = {Eddie-Luidy Imada and Diego Fernando Sanchez and Leonardo Collado-Torres and Christopher Wilks and Tejasvi Matam and Wikum Dinalankara and Aleksey Stupnikov and Francisco Lobo-Pereira and Chi-Wai Yip and Kayoko Yasuzawa and Naoto Kondo and Masayoshi Itoh and Harukazu Suzuki and Takeya Kasukawa and Chung Chau Hon and Michiel JL {de Hoon} and Jay W Shin and Piero Carninci and Andrew E. Jaffe and Jeffrey T. Leek and Alexander Favorov and Glória R Franco and Ben Langmead and Luigi Marchionni}, #> year = {2020}, #> journal = {Genome Research}, #> doi = {10.1101/gr.254656.119}, #> url = {https://doi.org/10.1101/gr.254656.119}, #> } ``` 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 *[usethis](https://CRAN.R-project.org/package=usethis)*, *[remotes](https://CRAN.R-project.org/package=remotes)*, *[sysreqs](https://github.com/r-hub/sysreqs)* and *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized to use [Bioconductor’s docker containers](https://www.bioconductor.org/help/docker/) and *[BiocCheck](https://bioconductor.org/packages/3.17/BiocCheck)*. - Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and *[covr](https://CRAN.R-project.org/package=covr)*. - The [documentation website](http://leekgroup.github.io/recount) is automatically updated thanks to *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*. - The code is styled automatically thanks to *[styler](https://CRAN.R-project.org/package=styler)*. - The documentation is formatted thanks to *[devtools](https://CRAN.R-project.org/package=devtools)* and *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*. For more details, check the `dev` directory. This package was developed using *[biocthis](https://bioconductor.org/packages/3.17/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> | <!-- Global site tag (gtag.js) - Google Analytics --> <script async src="https://www.googletagmanager.com/gtag/js?id=UA-78422749-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-78422749-1'); </script>