DEsingle - Githubissues

miaozhun commented 6 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/miaozhun/DEsingle

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 6 years ago

Hi @miaozhun

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: DEsingle
Type: Package
Title: Detecting Differentially Expressed Genes from single-cell RNA-seq data
Version: 0.99.0
Date: 2017-06-06
Author: Zhun Miao <miaoz13@mails.tsinghua.edu.cn>
Maintainer: Zhun Miao <miaoz13@mails.tsinghua.edu.cn>
Description: DEsingle is an R package for differential expression analysis of single-cell RNA-seq data.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports:
    stats,
    pscl (>= 1.4.9),
    gamlss (>= 4.4-0),
    VGAM (>= 1.0-2),
    MASS (>= 7.3-45),
    bbmle (>= 1.0.18),
    maxLik (>= 1.3-4)
Suggests:
    knitr,
    rmarkdown
VignetteBuilder: knitr
biocViews: DifferentialExpression, GeneExpression, SingleCell, RNASeq, Transcriptomics, Sequencing, Preprocessing, Software
RoxygenNote: 6.0.1

mtmorgan commented 6 years ago

An important part of Bioconductor packages is interoperability with other parts of the ecosystem. Before your package can be added to the review queue, it must be modified to work well with existing single cell packages, in particular the SingleCellExperiment data representation.

Bioconductor packages also require a fully-evaluated vignette that illustrates the package functionality in a comprehensive manner; your vignette might include description of the input data (are these raw counts? from a particular technology?) as well as interpretation (e.g., visualization) of results.

Please update your package to interoperate with the Bioconductor ecosystem, and expand the vignette. When you are ready, please post a brief comment here and I will moderate the package to be added to the review queue.

miaozhun commented 6 years ago

Hi, dear @mtmorgan ,

Thanks for your good suggestions. I have updated the DEsingle package and expanded the vignettes. Thank you very much!

Best wishes, Zhun

mtmorgan commented 6 years ago

OK. The SingleCellExperiment package should be included in the Suggests: field and the guidelines in the vignette should be to install it with biocLite("SingleCellExperiment"). The code chunk that actually illustrates SingleCellExperiment use should be evaluated, showing that your code actually works with this data structure.

bioc-issue-bot commented 6 years ago

A reviewer has been assigned to your package Learn What to Expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

bioc-issue-bot commented 6 years ago

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.

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

b7fe196 Update DESCRIPTION

bioc-issue-bot commented 6 years ago

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.

miaozhun commented 6 years ago

Hi, dear @mtmorgan ,

Thank you so much for the guidance! I modified the package according to your suggestions and bumped the package's version number. Thanks a lot!

Best wishes, Zhun

Liubuntu commented 6 years ago

Hi @miaozhun ,

Thank you for submitting you package to Bioconductor. A technical review will be given shortly.

Best, Qian

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

856499d Update DESCRIPTION

bioc-issue-bot commented 6 years ago

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.

Liubuntu commented 6 years ago

Hi @miaozhun ,

Thanks for your contribution to Bioconductor. Here is the initial technical review of your package. Please address each issue accordingly, comment back when you are ready for a second review or having any questions. Bump the version for a successful build.

DESCRIPTION

please Depends: R (>= 3.5.0).
Description is not clear enough. Please mention some following points to distinguish your package with other Bioconductor packages for scRNA-seq DEG analysis. In your manuscript: https://www.biorxiv.org/content/early/2017/09/08/173997,

DEsingle can distinguish three types of differential expression between two groups of single cells, with regard to differences in expression status, in expression abundances, and in both... Results showed that DEsingle outperforms existing methods for scRNA-seq DE analysis, and can reveal different types of DE genes that are enriched in different functions

Model and other scRNA-seq packages

You have mentioned comparing your package to others like: edgeR and DEGseq, did you compare your method with DESeq2?
with ZINB, did you compare your model with the bioconductor package ZINB-WaVE? Also check this post on Bioconductor support site for some packages mentioned there and check of your data for if it is real zero-inflated. https://support.bioconductor.org/p/74156/

R/
Could you DEsingle() function take singleCellExperiment class objects as input directly?
please put your data documentation for count and group into one separate R script, e.g., data.R, and use @rdname data for both data to generate just one manual file data.Rd for a clearer structure.

vignettes/

add sessionInfo() in the end of the vignette.
any visualization for your results?

man/

data documentation as said in the R section.

cheers! Qian

Liubuntu commented 6 years ago

The URL of bioconductor support site post is added on the previous comment. please check, thanks!

miaozhun commented 6 years ago

@Liubuntu Received, thanks!

Liubuntu commented 6 years ago

Hi @miaozhun ,

Bioconductor usually has a 2 week rule, and if no reponse (comments / questions / new commits or anything showing your are working to improve your package), the issue will be closed. It was 9 days ago for your last response. So please response within a week so that we can keep this issue open.

But if you think it's gonna take longer time for the fix or you are currently not available to update this package, please let us know. We can close the issue now, and whenever you are ready, we can reopen it.

Thanks, Qian

miaozhun commented 6 years ago

Hi @Liubuntu ,

Thanks a lot for your reminding. I have addressed most of the issues accordingly. And please see the details blow.

DESCRIPTION

Depends: R (>= 3.4.0). (Addressed).
Clearer description. (Addressed).

Model and other scRNA-seq packages

Compare DEsingle with DESeq2. (Unfinished yet). Actually, I have compared DEsingle with DESeq then and found that for large sample size DESeq will collapse. I'll compare DEsingle with DESeq2 later and add the results ASAP.
Compare with ZINB-WaVE. (Addressed). Actually, the most important point of our package is to estimate the ratio of "real zeros" and "dropout zeros" in single-cell RNA-seq (scRNA-seq) data and define and detect 3 types of DE genes accordingly. While the ZINB-WaVE package focus on the low-dimensional representations of scRNA-seq data, though we both employed the ZINB model.
Check the data is real zero-inflated. (Addressed). The answer is yes. For the data I used and for scRNA-seq data, a negative binomial model wouldn't enough for account all the zeros, there exists inflated zeros.

R/

DEsingle() function take singleCellExperiment class objects as input directly. (Addressed). I have modified the code and vignettes, and now DEsingle() could accept singleCellExperiment class objects as input directly.
Documentation for count and group together. (Addressed).

vignettes/

Add sessionInfo() in the end of the vignette. (Addressed).
Visualization for results. (Addressed). Actually, users could plot the heatmap of the DE genes DEsingle found using heatmap() function or heatmap.2() function in gplots, as we did in our manuscript. And we added this in our vignettes.

man/

Data documentation as said in the R section. (Addressed).

Many thanks for your help!

Best regards, Zhun

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

e87098a Update DESCRIPTION

bioc-issue-bot commented 6 years ago

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: "TIMEOUT, 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.

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

5ad4732 Update DESCRIPTION

bioc-issue-bot commented 6 years ago

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.

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

72d5a75 Update DESCRIPTION

bioc-issue-bot commented 6 years ago

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.

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

f3acd66 Update DESCRIPTION

bioc-issue-bot commented 6 years ago

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.

miaozhun commented 6 years ago

Hi, dear @Liubuntu ,

I have also added DESeq2 to the comparison of DE analysis methods on single-cell RNA-seq data, and found that DEsingle also have advantages over DESeq2. Here is the ROC curve.

roc curve

I'll also add the results to our manuscript and update the article on bioRxiv. Besides, our manuscript is also under the review process of Bioinformatics now. Thanks a lot for your help!

Best wishes, Zhun

Liubuntu commented 6 years ago

Hi @miaozhun ,

Thanks for your updates! A 2nd review will be given shortly.

Best, Qian

Liubuntu commented 6 years ago

Hi @miaozhun ,

Thank you for your updates. Here are some additional issues that are mostly just cosmetic. Please seek to fixed them ASAP and your package should be good to go. Cheers!

DESCRIPTION

typo: Should ...different expression status (DEs)... be ...differential expression status (DEs) to be consistent with other terms?
Else looks good!

R

Since you function DEsingle(counts=) could handle singleCellExperiment objects as input, you should also specify this in the argument documentation and the function description.

man

typo in "TestData.Rd": \title{TestData: A test dataset for DEsinge}, should be {... for DEsingle}

vignettes

IMPORTANT: please add a section called Installation between Inroduction and Input, and show to users how to download and library this package as it is already available in Bioconductor. E.g., to use BiocInstaller function for downloading.
```
BiocInstaller::biocLite("DEsingle")                                                                    
```
You can also choose to add a subsection for installing the developmental version from github, e.g.,
```
devtools::install_github("miaozhun/DEsingle")
```

Best, Qian

bioc-issue-bot commented 6 years ago

Received a valid push; starting a build. Commits are:

9c5aac6 Update DESCRIPTION

bioc-issue-bot commented 6 years ago

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.

miaozhun commented 6 years ago

Hi, dear Qian @Liubuntu ,

Thank you very much for your effort and guidance to the improvement of the package! I'm really appreciate your help.

Now I have addressed all the issues mentioned above. Please see blow for the details.

DESCRIPTION

typo: Should ...different expression status (DEs)... be ...differential expression status (DEs) to be consistent with other terms?

Thank you. Actually, it's not a typo. We want to use the word different to represent the on/off status of a gene, and the two statuses are discrete and totally different. While we use differential in the other two terms to represent classical continuous differential expression.

R

Since your function DEsingle(counts=) could handle SingleCellExperiment objects as input, you should also specify this in the argument documentation and the function description.

Documentation of the help page is updated.

man

typo in "TestData.Rd": \title{TestData: A test dataset for DEsinge}, should be {... for DEsingle}

The typo is corrected now.

vignettes

IMPORTANT: please add a section called Installation between Inroduction and Input, and show to users how to download and library this package as it is already available in Bioconductor.

Section Installation is added in the vignettes.

Thanks again for your help! Cheers!

Best regards, Zhun

Liubuntu commented 6 years ago

Hi @miaozhun ,

Thank you for your quick fix. I will accept the package now. But there is one more little thing to do, Can you add a TOC for your vignette after the acceptance? check here: https://rmarkdown.rstudio.com/html_document_format.html

Best, Qian

bioc-issue-bot commented 6 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

miaozhun commented 6 years ago

Hi, dear Qian @Liubuntu ,

Thanks for your good suggestions. I have added the TOC for the vignettes now.

Best wishes, Zhun

mtmorgan commented 6 years ago

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/miaozhun.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 biocLite(\"DEsingle\"). The package 'landing page' will be created at

https://bioconductor.org/packages/DEsingle

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.

Bioconductor / Contributions

DEsingle #653

DESCRIPTION

Model and other scRNA-seq packages

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Model and other scRNA-seq packages

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