Closed jasonratcliff closed 4 years ago
Hi @jasonratcliff
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: aggregateBioVar
Type: Package
Title: Differential Gene Expression Analysis for Multi-subject scRNA-seq
Version: 0.99.0
Authors@R: c(
person(given = "Jason", family = "Ratcliff",
email = "jason-ratcliff@uiowa.edu", role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-7079-334X")),
person(given = "Andrew", family = "Thurman",
email = "andrew.thurman2@gmail.com", role = "aut"),
person(given = "Michael", family = "Chimenti",
email = "michael-chimenti@uiowa.edu", role = "ctb"),
person(given = "Alejandro", family = "Pezzulo",
email = "alejandro-pezzulo@uiowa.edu", role = "ctb")
)
URL: https://github.com/jasonratcliff/aggregateBioVar
BugReports: https://github.com/jasonratcliff/aggregateBioVar/issues
Description: For single cell RNA-seq data collected from more than
one subject (e.g. biological sample or technical replicates),
this package contains tools to summarize single cell gene expression
profiles at the level of subject. A SingleCellExperiment object is taken as
input and converted to a list of SummarizedExperiment objects, where each
list element corresponds to an assigned cell type.
The SummarizedExperiment objects contain aggregate gene-by-subject
count matrices and inter-subject column metadata for individual subjects
that can be processed using downstream bulk RNA-seq tools.
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
biocViews: Software, SingleCell, RNASeq, Transcriptomics,
Transcription, GeneExpression, DifferentialExpression
Depends:
R (>= 4.0)
Imports:
stats,
methods,
S4Vectors,
SummarizedExperiment,
SingleCellExperiment,
Matrix,
tibble,
rlang
Suggests:
BiocStyle,
magick,
knitr,
rmarkdown,
testthat,
BiocGenerics,
DESeq2,
magrittr,
dplyr,
ggplot2,
cowplot,
ggtext,
RColorBrewer,
pheatmap,
viridis
I was curious how this package differs to what is offered by scuttle and scran (e.g., scuttle::aggregateAcrossCells()
and scran::pseudoBulkDGE()
) by @LTLA and the muscat package by @HelenaLC but couldn't find anything.
I think such a comparison would be helpful for users deciding whether to use aggregateBioVar.
Thanks for the suggestion @PeteHaitch. I agree that would be a useful addition to the documentation. I noticed a recent relevant Bioconductor support post (https://support.bioconductor.org/p/133569/) as I was getting ready to submit that touches on this issue. It looks like there's similarity in how counts are handled with muscat, but instead of multiple assays for each cell type in one SingleCellExperiment
return object, aggregateBioVar returns a list of individual SummarizedExperiment
objects each with summarized metadata. This is my first go at package development associated with a manuscript submission, so I appreciate the feedback.
A reviewer has been assigned to your package. Learn what to expect during the review process.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
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/aggregateBioVar
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@hpages, a quick question about the warning. It looks like a Windows build warning related to Rd cross-references. I'm using roxygen2 (v7.1.1) to generate Rd files, and it looks like the problem stems from the following lines:
\link[SummarizedExperiment]{assay}
\link[SummarizedExperiment]{colData}
Do you know have any suggestion for addressing that warning? It appears to be Windows specific.
Received a valid push on git.bioconductor.org; starting a build for commit id: aabc00d1c37b983c72f361aaef1fa39d0fd6ecc2
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/aggregateBioVar
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
For windows you need to link the file as it does not recognize alias. I believe something like the following should fix \link[SummarizedExperiment:SummarizedExperiment-class]{colData}
cheers
Received a valid push on git.bioconductor.org; starting a build for commit id: 94bfce9e6577fc55d76bdd0ecdebd139b656c967
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/aggregateBioVar
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Looks like that worked, thanks!
Thanks for the submission.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
The master branch of your GitHub repository has been added to Bioconductor's git repository.
To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/jasonratcliff.keys is not empty), then no further steps are required. Otherwise, do the following:
See further instructions at
https://bioconductor.org/developers/how-to/git/
for working with this repository. See especially
https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
to keep your GitHub and Bioconductor repositories in sync.
Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at
https://bioconductor.org/checkResults/
(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("aggregateBioVar")
. The package 'landing page' will be created at
https://bioconductor.org/packages/aggregateBioVar
If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Confirm the following by editing each check box to '[x]'
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[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.
I am familiar with the essential aspects of Bioconductor software management, including:
For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.