Closed jgilis closed 3 years ago
Hi @jgilis
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: satuRn
Type: Package
Title: Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Date: 2021-01-26
Version: 0.99.5
Authors@R: c(person("Jeroen", "Gilis", role = c("aut","cre"),
email = "jeroen.gilis@ugent.be"),
person("Kristoffer", "Vitting-Seerup", role = "ctb",
email = "kristoffer.vittingseerup@bio.ku.dk"),
person("Koen","Van den Berge", role = "ctb",
email = "koen.vandenberge@ugent.be"),
person("Lieven","Clement", role="ctb",
email = "Lieven.Clement@ugent.be"))
Description: satuRn provides a higly performant and scalable framework for performing
differential transcript usage analyses. The package consists of three main functions.
The first function, fitDTU, fits quasi-binomial generalized linear models that model
transcript usage in different groups of interest. The second function, testDTU, tests
for differential usage of transcripts between groups of interest. Finally, plotDTU
visualizes the usage profiles of transcripts in groups of interest.
Depends: R (>= 4.0)
Imports: locfdr,
SummarizedExperiment,
BiocParallel,
limma,
pbapply,
ggplot2,
boot,
Matrix,
stats,
methods,
graphics
Suggests:
knitr,
rmarkdown,
testthat,
covr,
BiocStyle,
AnnotationHub,
ensembldb,
edgeR,
DEXSeq,
stageR,
DelayedArray
VignetteBuilder: knitr
Collate:'data.R' 'satuRn-framework.R' 'allGenerics.R'
'accessors.R' 'fitDTU.R' 'testDTU.R' 'plotDTU.R'
License: Artistic-2.0
URL: https://github.com/statOmics/satuRn
BugReports: https://github.com/statOmics/satuRn/issues
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.1
biocViews:
Regression,
ExperimentalDesign,
DifferentialExpression,
GeneExpression,
RNASeq,
Sequencing,
Software,
SingleCell,
Transcriptomics,
MultipleComparison,
Visualization
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/satuRn
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 3641a9a8c2300c7d3ae0887bc0a88f3d6e921c07
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/satuRn
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@jgilis - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review. Overall, this is a really well put together package. Very well organized, written, and documented. I have just a few points below.
eval = FALSE
.if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("satuRn")
eval = FALSE
?[x] REQUIRED: Unexported object imported by a ':::' call: 'locfdr::locmle'.
[ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 99 lines that are > 80 characters long.
[ ] SUGGESTION: For formatting reaosns, consider multiples of 4 spaces for line indents. There are 22 lines that are not.
Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: c9fd2bee47c4eb3b1cf5c8351fb4b5e94855a0e6
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/satuRn
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear Kayla,
Thank you very much for your kind words in the previous review. This is the first time I submit to Bioconductor and even the first time I published an R package for external use. The fact that the package was immediately quite close to the desired output really is a testament to the convenience of the BiocCheck
package and the extensive documentation for the submission procedure as provided by Bioconductor.
That said, I recently made a new push to accommodate your remarks. All requirements should now be met. I also worked on meeting your suggestions, reducing the number of long lines and troublesome indents. However, some troublesome indents remain (also upon running styler
), in particular in the man pages created by roxygen2
.
Looking forward to completing the submission procedure,
Kind regards,
Jeroen
@jgilis - Thank you for making the required changes and attempting to clear up the suggestions as well. I have looked over the changes and everything looks good. I'm more than happy to accept the package.
Best, Kayla
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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