bioc-issue-bot
commented
7 years ago Hi @lcolladotor
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: recountWorkflow
Title: recount workflow: accessing over 70,000 human RNA-seq samples with
Bioconductor
Version: 0.99.0
Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"),
email = "lcollado@jhu.edu"), person("Abhinav", "Nellore", role = "ctb",
email = "anellore@gmail.com"), person(c("Andrew", "E."), "Jaffe",
role = "ctb", email = "andrew.jaffe@libd.org"))
Description: The recount2 resource is composed of over 70,000 uniformly
processed human RNA-seq samples spanning TCGA and SRA, including GTEx. The
processed data can be accessed via the recount2 website and the recount
Bioconductor package. This workflow explains in detail how to use the
recount package and how to integrate it with other Bioconductor packages for
several analyses that can be carried out with the recount2 resource. In
particular, we describe how the coverage count matrices were computed in
recount2 as well as different ways of obtaining public metadata, which can
facilitate downstream analyses. Step-by-step directions show how to do a
gene level differential expression analysis, visualize base-level genome
coverage data, and perform an analyses at multiple feature levels. This
workflow thus provides further information to understand the data in
recount2 and a compendium of R code to use the data.
Depends: R (>= 3.4.0)
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
biocViews: WorkflowStep, Coverage, DifferentialExpression, GeneExpression,
RNASeq, Sequencing, Software, DataImport
VignetteBuilder: knitr
Imports:
recount,
GenomicRanges,
limma,
edgeR,
DESeq2,
regionReport (>= 1.10.2),
clusterProfiler,
org.Hs.eg.db,
gplots,
derfinder,
rtracklayer,
GenomicFeatures,
bumphunter,
derfinderPlot,
devtools,
rmarkdown,
knitcitations,
BiocStyle,
knitr
NeedsCompilation: no
Workflow: true
URL: https://github.com/LieberInstitute/recountWorkflow
BugReports: https://support.bioconductor.org/t/recountWorkflow/
lcolladotor
mtmorgan
vobencha
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Note that this package is a workflow and not a software package.
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[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
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