Document that the data is now hosted at https://registry.opendata.aws…

…/recount/ in addition to IDIES
LieberInstitute · Jan 11, 2023 · 7c4e68e · 7c4e68e
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diff --git a/README.Rmd b/README.Rmd
@@ -93,12 +93,12 @@ The `ReCount` family involves the following teams:
 * [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 [SciServer from IDIES at JHU](https://www.sciserver.org/)
+* 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="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> |
 
 
 <script type='text/javascript' id='clustrmaps' src='//cdn.clustrmaps.com/map_v2.js?cl=ffffff&w=300&t=n&d=4xd7F6p1BfdRypx-yEodrXiKhC0xvF0bJJywqR8rMKQ'></script>

diff --git a/README.md b/README.md
@@ -4,21 +4,34 @@
 # recount3 <img src="man/figures/logo.png" align="right" width="200px" >
 
 <!-- badges: start -->
-[![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/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/LieberInstitute/recount3/actions)
-[![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)
+
+[![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/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/LieberInstitute/recount3/actions)
+[![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)
 <!-- badges: end -->
 
-The *[recount3](https://bioconductor.org/packages/3.15/recount3)*
+The *[recount3](https://bioconductor.org/packages/3.16/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
@@ -30,7 +43,7 @@ R/Bioconductor package and other tools are related to each other.
 ## Documentation
 
 For more information about
-*[recount3](https://bioconductor.org/packages/3.15/recount3)* check the
+*[recount3](https://bioconductor.org/packages/3.16/recount3)* check the
 vignettes [through
 Bioconductor](http://bioconductor.org/packages/recount3) or at the
 [documentation website](http://lieberinstitute.github.io/recount3).
@@ -39,7 +52,7 @@ Bioconductor](http://bioconductor.org/packages/recount3) or at the
 
 Get the latest stable `R` release from
 [CRAN](http://cran.r-project.org/). Then install
-*[recount3](https://bioconductor.org/packages/3.15/recount3)* from
+*[recount3](https://bioconductor.org/packages/3.16/recount3)* from
 [Bioconductor](http://bioconductor.org/) using the following code:
 
 ``` r
@@ -59,30 +72,32 @@ Please run this yourself to check for any updates on how to cite
 ``` r
 print(citation("recount3"), bibtex = TRUE)
 #> 
-#> Collado-Torres L (2022). _Explore and download data from the recount3
-#> project_. doi: 10.18129/B9.bioc.recount3 (URL:
-#> https://doi.org/10.18129/B9.bioc.recount3),
-#> https://github.com/LieberInstitute/recount3 - R package version 1.5.1,
-#> <URL: http://www.bioconductor.org/packages/recount3>.
+#> To cite package 'recount3' in publications use:
+#> 
+#>   Collado-Torres L (2023). _Explore and download data from the recount3
+#>   project_. doi:10.18129/B9.bioc.recount3
+#>   <https://doi.org/10.18129/B9.bioc.recount3>,
+#>   https://github.com/LieberInstitute/recount3 - R package version
+#>   1.9.1, <http://www.bioconductor.org/packages/recount3>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
 #>     title = {Explore and download data from the recount3 project},
 #>     author = {Leonardo Collado-Torres},
-#>     year = {2022},
+#>     year = {2023},
 #>     url = {http://www.bioconductor.org/packages/recount3},
-#>     note = {https://github.com/LieberInstitute/recount3 - R package version 1.5.1},
+#>     note = {https://github.com/LieberInstitute/recount3 - R package version 1.9.1},
 #>     doi = {10.18129/B9.bioc.recount3},
 #>   }
 #> 
-#> Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL,
-#> Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L,
-#> Hansen KD, Langmead B (2021). "recount3: summaries and queries for
-#> large-scale RNA-seq expression and splicing." _Genome Biol_. doi:
-#> 10.1186/s13059-021-02533-6 (URL:
-#> https://doi.org/10.1186/s13059-021-02533-6), <URL:
-#> https://doi.org/10.1186/s13059-021-02533-6>.
+#>   Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL,
+#>   Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L,
+#>   Hansen KD, Langmead B (2021). "recount3: summaries and queries for
+#>   large-scale RNA-seq expression and splicing." _Genome Biol_.
+#>   doi:10.1186/s13059-021-02533-6
+#>   <https://doi.org/10.1186/s13059-021-02533-6>,
+#>   <https://doi.org/10.1186/s13059-021-02533-6>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
@@ -97,7 +112,7 @@ print(citation("recount3"), bibtex = TRUE)
 ```
 
 Please note that
-*[recount3](https://bioconductor.org/packages/3.15/recount3)* was only
+*[recount3](https://bioconductor.org/packages/3.16/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.
@@ -111,27 +126,26 @@ 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/3.15/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://lieberinstitute.github.io/recount3) 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)*.
+- 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/3.16/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://lieberinstitute.github.io/recount3)
+  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.
 
@@ -143,29 +157,31 @@ 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) | *[recount](https://bioconductor.org/packages/3.15/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)                                                              | *[recount3](https://bioconductor.org/packages/3.15/recount3)* |
+| 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) | *[recount](https://bioconductor.org/packages/3.16/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)                                                              | *[recount3](https://bioconductor.org/packages/3.16/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 [SciServer from IDIES 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> |
+- [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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