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epiregulon
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- Repository: https://github.com/xiaosaiyao/epiregulon
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Hi @TomVuod
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: epiregulon
Title: Gene regulatory network inference from single cell epigenomic data
Version: 0.99.0
Date: 2023-11-21
Authors@R:
c(person(given = "Xiaosai", family = "Yao", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0001-9729-0726")),
person(given = "Tomasz", family = "Włodarczyk", role = c("aut"), email = "[email protected]", comment = c(ORCID = "0000-0003-1554-9699")),
person(given = "Aaron", family = "Lun", role=c("aut"), email="[email protected]"),
person(given = "Shang-Yang", family = "Chen", role = "aut", email = "[email protected]"))
Description: Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.
License: file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports:
BiocFileCache,
BiocParallel,
Matrix,
Rcpp,
S4Vectors,
SummarizedExperiment,
bluster,
checkmate,
entropy,
lifecycle,
methods,
scran,
scuttle,
stats,
utils,
scMultiome,
GenomeInfoDb,
GenomicRanges,
AUCell,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10,
motifmatchr
Depends:
R (>= 4.2.0),
SingleCellExperiment
Suggests:
knitr,
rmarkdown,
parallel,
BiocStyle,
testthat (>= 3.0.0),
coin,
scater
LinkingTo: Rcpp
VignetteBuilder: knitr
URL: https://github.com/xiaosaiyao/epiregulon/
biocViews: GeneExpression, Transcription, ChipOnChip, DifferentialExpression, GeneTarget, Normalization, GraphAndNetwork
Config/testthat/edition: 3
BugReports: https://github.com/xiaosaiyao/epiregulon/issues
I had a quick look. I think it would be helpful to readers/reviewers if the vignette referenced the online book https://xiaosaiyao.github.io/epiregulon.book/ . The vignette introduction is too terse and does not explain terms used.
Thank you @vjcitn. We've now added the reference to the book in the vignette
We normally don't allow data to be hosted on an untrusted source like github, dropbox, etc. Can the motif data be submitted to a more stable location like zenodo?
Hi @lshep chromVARmotifs is a highly cited and widely used package. https://github.com/GreenleafLab/chromVARmotifs
We prefer to download directly from the source. I hope that's acceptable.
The chromVARmotifs has not been updated in 7 years, has several open issues with no response, and there is no set of action to perform any sort of systematic checking (like R CMD build, R CMD check, etc.) which is why Bioconductor does not allow github only packages to be listed as dependencies and only allows packages on CRAN or Bioconductor to be a dependency. The same is true for data pulled from those sources; there is no clear indication of maintenance or keeping data up-to-date. chromVARmotifs should submit their package to CRAN or Bioconductor; or at least add their data to a public curation site like zenodo, microsoft data lakes, or public S3 bucket.
Hello @Ishep, epiregulon in no longer dependent on chromVARmotifs repository. The data sets have been included in scMultiome Bioc package and are retrieved from AnnotationHub (commit 355c2f9). We are now waiting for the release of rhdf5 package v2.47.4 since the bug in the current version causes error when vignette is being built (https://github.com/grimbough/rhdf5/issues/139).
It looks like the builders missed the Sat build. I would expect the new version of rhdf5 to be available later today, after today's builds and propagation, once that happens I'll re-evaluate the package for the next stage of review.
You still have a library call to chromVARmotifs in the documentation. Please remove. Since you now call AnnotationHub/ExperimentHub you will likely need to list them in your DESCRIPTION file appropriately in Suggests
Can you use an OSI-approved license for this package? https://opensource.org/licenses/
Fiscal sponsorship through NumFocus obligates us to support software packages with open source licensing.
@vjcitn I just consulted with our legal team. We would prefer to stick to our existing license which gives open access to all academic centers. The only restriction we impose is for commercial entities. I hope our license is compliant and will not block our submission to BioC.
https://contributions.bioconductor.org/license.html is very clear that restrictive licensing (e.g., academic only) is not possible. The project fiscal sponsorship has required us to avoid restrictive licensing. I think that if you cannot use open licensing we probably shouldn't pursue this submission, really sorry about that.
@vjcitn regretfully we can't change the LICENCE (at least for now) and have to withdraw this submission. FYI @TomVuod
I am sorry about this. I will have further discussions with NumFocus to see if there is a way forward.
@vjcitn we have received the green light to change the license. It is now MIT.
FYI @TomVuod
I've updated my source archive. A few questions to be resolved before review begins.
-
getTFMotifInfodoc says#' motif information is annotated by cisbp from [chromVARmotifs](https://github.com/GreenleafLab/chromVARmotifs)what does "is annotated" mean? Are there real-time queries to chromVARmotifs? Was a snapshot made? If so what kind of provenance information can be provided? -
Vignette section 4.1 has
First, we retrieve the information of TF binding sites collected from Cistrome and ENCODE ChIP-seq, which are hosted on Genomitory.What is Genomitory? -
I'd say the introduction of the vignette is too terse, "AR" should be spelled out too. Give a brief account of the scientific purpose of the package in the vignette introduction.
-
4.4 has
"A long format dataframe, representing the inferred regulons, is then generated. The dataframe consists of three columns:
tf (transcription factor) target gene peak to gene correlation between tf and target gene"
but the code output does not produce such a data frame?
regulon <- getRegulon(p2g = p2g, overlap = overlap, aggregate = FALSE)
regulon
#> DataFrame with 746875 rows and 10 columns
#> idxATAC chr start end idxRNA target
#> <integer> <character> <integer> <integer> <integer> <character>
#> 1 37 chr1 1020509 1021009 22 AL645608.4
#> 2 37 chr1 1020509 1021009 22 AL645608.4
#> 3 37 chr1 1020509 1021009 22 AL645608.4
- the vignette concludes with
head(score.combine)but the output in chrome browser looks like
@vjcitn Thank you for reviewing the vignette. I apologize for not updating some of the text earlier. The vignette should be cleaned up. I provided further details on the package in the introduction. Let me know should you require more changes.
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". 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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): epiregulon_0.99.6.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/epiregulon to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
@lshep do I have the permission to push to upstream? or only @TomVuod has?
The BiocCredentials account is now wrong and corrupt for your two account. We assume the submitter is the maintainer and match the submitter github userid with the maintainer email in the DESCRIPTION. So now [email protected] is associated with TomVuod and not xiaosaiyao . I will delete and reset the account and send activation instructions. Do you both need push access?
Received a valid push on git.bioconductor.org; starting a build for commit id: 60eea5bc572011faf6006a985e20376f315fc5db
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". 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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): epiregulon_0.99.7.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/epiregulon to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.