scPipe: a package for single cell RNA-seq data processing and quality control

LuyiTian 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/LuyiTian/scPipe

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:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

LuyiTian commented 6 years ago

This is a resubmission of my package.

It now uses the SingleCellExperiment as the base class and works well with other packages like scater and scran. It also supports the recently released official bam tags for the UMI and cell barcode:https://github.com/samtools/hts-specs/pull/200#event-1221322336.

We have decided not to change the package name because we think it covers the main point of this package, which is a preprocessing pipeline of scRNA-seq. Apart from that, all other comments in the previous submission have been followed.

bioc-issue-bot commented 6 years ago

Dear @LuyiTian ,

You (or someone) has already posted that repository to our tracker.

See https://github.com/Bioconductor/Contributions/issues/489

You cannot post the same repository more than once. I am closing this issue.

bioc-issue-bot commented 6 years ago

Hi @LuyiTian

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: scPipe
Title: pipeline for single cell RNA-seq data analysis
Version: 0.99.20
Type: Package
Maintainer: Luyi Tian <tian.l@wehi.edu.au>
Author: Luyi Tian
Authors@R: c(person("Luyi", "Tian", role=c("aut", "cre"),
        email="tian.l@wehi.edu.au"), person("Shian", "Su",
        role=c("aut"), email="su.s@wehi.edu.au"), person("Matt",
        "Ritchie", role=c("ctb"),
        email="mritchie@wehi.edu.au"),  person("Shalin",
        "Naik", role=c("ctb"),
        email="naik.s@wehi.edu.au"))
biocViews: Software, Sequencing, RNASeq, GeneExpression, SingleCell, Visualization,
        SequenceMatching, Preprocessing, QualityControl, GenomeAnnotation
Description: to process single cell RNA-seq data from fastq to gene counting matrix. it can process data generated by CEL-seq, MARS-seq, Drop-seq and SMART-seq.
Depends: R (>= 3.4), ggplot2, methods, SingleCellExperiment
LinkingTo: Rcpp, Rhtslib, zlibbioc
Imports: Rhtslib, biomaRt, GGally, MASS, mclust, Rcpp (>= 0.11.3), reshape, BiocGenerics, robustbase, scales, utils, stats, S4Vectors, SummarizedExperiment
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: yes
URL: https://github.com/LuyiTian/scPipe
BugReports: https://github.com/LuyiTian/scPipe
Suggests: knitr, rmarkdown,
    testthat, Rsubread
VignetteBuilder: knitr

bioc-issue-bot commented 6 years ago

Your package has been approved for building. Your package is now submitted to our queue.

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: "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 following build report for more details:

http://bioconductor.org/spb_reports/scPipe_buildreport_20170924101824.html

bioc-issue-bot commented 6 years ago

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

ac506d1 Update doc, fix warning Update doc to fix the war...

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/scPipe_buildreport_20170925003626.html

bioc-issue-bot commented 6 years ago

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

0c757dd 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: "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 following build report for more details:

http://bioconductor.org/spb_reports/scPipe_buildreport_20170925100912.html

bioc-issue-bot commented 6 years ago

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

592d502 fix win check error

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 following build report for more details:

http://bioconductor.org/spb_reports/scPipe_buildreport_20170925104217.html

LuyiTian commented 6 years ago

Hi @hpages I think all errors and warnings are fixed and it can be reviewed now. :)

vobencha commented 6 years ago

Changing reviewer to vobencha since I reviewed of the original submission.

vobencha commented 6 years ago

Hi,

The package looks much better. Thank you for reusing SingleCellExperiment. A few comments below.

1) man pages for datasets

Please describe the matrices. Are there column/row names and what do they mean? Were the data QC'd? The souce simply lists a person's name - better to have a web site or paper reference. Please include as many details as you can about the data.

Also add an \examples section where you show how to load and manipulate the data.

2) There are several typos in the vignette. You may want to run a spell checker.

3) Please remove LazyData = true. This rarely proves to be a good thing. In our experience it only slows down the loading of packages with large data.

Valerie

vobencha commented 6 years ago

I just edited my review to include a comment on LazyData.

bioc-issue-bot commented 6 years ago

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

565ddb7 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 following build report for more details:

http://bioconductor.org/spb_reports/scPipe_buildreport_20171011020115.html

bioc-issue-bot commented 6 years ago

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

3570523 Final commit before second review

LuyiTian commented 6 years ago

Hi, @vobencha I have made changes according to your review.

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 following build report for more details:

http://bioconductor.org/spb_reports/scPipe_buildreport_20171011041014.html

vobencha commented 6 years ago

Thank you. Package is approved.

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 sent to the maintainer email address in the next several days.

Thank you for contributing to Bioconductor!

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/LuyiTian.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(\"scPipe\"). The package 'landing page' will be created at

https://bioconductor.org/packages/scPipe

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

scPipe: a package for single cell RNA-seq data processing and quality control #489