Closed rx-li closed 1 year ago
Hi @rx-li
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: partCNV
Type: Package
Title: Infer locally aneuploid cells using single cell RNA-seq data
Version: 0.99.0
Authors@R: c(
person(given="Ziyi", family="Li", email="zli16@mdanderson.org", role=c("aut", "cre", "ctb")),
person(given="Ruoxing", family="Li", email="ruoxingli@outlook.com", role="ctb"))
Description: This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).
Imports: stats, data.table, depmixS4, Seurat, Matrix, GenomicRanges
Suggests: BiocStyle, rmarkdown, knitr, IRanges
VignetteBuilder: knitr
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.1
biocViews: Software, CopyNumberVariation, HiddenMarkovModel
Thanks for this submission. It needs some work before we review. 1) example(partCNV) doesn't really do anything. 2) you include cytoband addresses that are 0 based, that come from UCSC, but Bioconductor already has cytobands for hg38 in a GRanges in AH53178, adhering to the 1-based convention of Bioconductor, 3) when I look at the vignette, the colors in the UMAP visualizations do not have a key visible.
Dear Vince,
Thanks so much for the insights. I have updated the package:
Please let me know if you have any questions.
Best regards, Ruoxing
On Tue, Dec 6, 2022 at 4:14 AM Vince Carey @.***> wrote:
Thanks for this submission. It needs some work before we review. 1) example(partCNV) doesn't really do anything. 2) you include cytoband addresses that are 0 based, that come from UCSC, but Bioconductor already has cytobands for hg38 in a GRanges in AH53178, adhering to the 1-based convention of Bioconductor, 3) when I look at the vignette, the colors in the UMAP visualizations do not have a key visible.
— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/2861#issuecomment-1339086799, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASV6ODXZFWF6P3NFMVV4BVDWL4GZNANCNFSM6AAAAAASN5A5RQ . You are receiving this because you were mentioned.Message ID: @.***>
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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.
Congratulations! The package built without errors or warnings on all platforms.
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Remember: if you submitted your package after July 7th, 2020,
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Hi @rx-li
Thanks for the submission the package looks interesting a useful. Having a first quick pass through the package there are some aspect that need addressing before a more detailed review.
Bioconductor objects:
Whilst we are happy for methods to also work on Seurat object we require that the package build on the BioC infrastructure. If I've understood your package correctly it could start from a SingeCellExperiment
object instead? Do correct me if there a more appropriate object. I imagine getting your code to work with Bioc object will change quite a lot of the vignette and code so its worth addressing the issues first
Other issues:
Looking forward to including this package in the Bioc family
Received a valid push on git.bioconductor.org; starting a build for commit id: e3e0bb52e5915ce22d3214672f5f55dcfe92e2f1
Dear @ococrook,
Thanks so much for your review and comments.
You are right about the SingleCellExperiment
object. If we start from the SingeCellExperiment
object, counts can be normalized and log transformed manually, and I have included the normalization method in the vignette.
For the other issues, please find the one-by-one responses below:
Thanks again for your help. Looking forward to your reply.
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: "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. 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
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to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Sorry did you have a look through the build report and fix the Errors? http://staging.bioconductor.org:8000/job/18410/
You also need to state the R version of the code.
@rx-li
The package still builds with Errors, we can close the issue until you have time address these at which point we can re-open the issue if necessary?
@ococrook I am so sorry that I overlooked the email regarding the issue. I will address it ASAP. Thanks so much.
Received a valid push on git.bioconductor.org; starting a build for commit id: ea132b281354fa04fc89474296ac7fcaa8588fe8
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: "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. 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
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@rx-li
Are you subscribed to the mailing list?
I don't see the maintainer email registered. If you tried to register, there is normally a confirmation email sent. It can sometimes be marked as spam/junk. Please check those folders for the confirmation email.
Received a valid push on git.bioconductor.org; starting a build for commit id: b64531cd32b6ba4f6a282428e96ef5a3bb35278e
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/partCNV
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
The package only cursorily engages with SingelCellExperiment
as a passing comment. For the package to be accepted to Bioconductor it needs to be more carefully integrated into the workflow.
Dear @ococrook
Thanks for your comment. I will add more steps on how to start from SingelCellExperiment
.
Best regards, Ruoxing
Brilliant, thank you!
Received a valid push on git.bioconductor.org; starting a build for commit id: c721e6e5ce29217c49492e317842d337bcd40cd2
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/partCNV
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: d2b8a123855c599b682727d547c2966e6f2b0fa7
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/partCNV
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: 941ff806a8a76df7c567fa64c30cafdf2b00349a
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/partCNV
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: 5b4d310f93c40f7ce87308916d5cf9c2465d01c3
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/partCNV
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: 25cd2263d4e8e2f30fac386af51703424c18175b
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/partCNV
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @ococrook,
Good afternoon.
I have added a function which can normalize the counts for a SingleCellExperiment
object, and its results can be used in the analysis.
Please let me know if anything else is needed.
Thanks, Ruoxing
Great, thank you Ruoxing.
Can you add Bioconductor install instructions and then I can accept the package
Received a valid push on git.bioconductor.org; starting a build for commit id: fb477d13ce7589bbdb1397eb948c5e9b0172ebb3
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/partCNV
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
The install instructions are added. Thanks so much, @ococrook!
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
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Dear @ococrook ,
Thanks for accepting our package.
I am wondering where I can access the Bioconductor webpage of the package. I saw that the package had been nightly built, but I did not find the URL for the package.
Best regards, Ruoxing
Hi @rx-li,
It will appear it due course, it can take sometime for the maintainers to set-up the webpage. Youll be able to search here when it's ready: https://www.bioconductor.org/packages/devel/BiocViews.html#___Software. I suspect if should take a few more days.
Best wishes, Olly
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