crisprDesign #2647

Jfortin1 · 2022-04-26T15:21:54Z

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bioc-issue-bot · 2022-04-26T15:21:56Z

Hi @Jfortin1

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: crisprDesign
Title: Comprehensive design of CRISPR gRNAs for nucleases and base editors
Version: 0.99.77
Authors@R: c(
    person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre")),
    person("Luke", "Hoberecht", email = "lukehob3@gmail.com", role = c("aut"))
    )
Description: 
    Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This 
    includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS
    contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR 
    modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, 
    CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including
    DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are
    also supported. gRNA design can be performed on reference genomes, transcriptomes,
    and custom DNA and RNA sequences. 
Depends: R (>= 4.2.0),
    crisprBase (>= 0.99.15)
Imports:
    AnnotationDbi,
    BiocGenerics,
    Biostrings,
    BSgenome,
    crisprBowtie (>= 0.99.8),
    crisprScore (>= 0.99.24),
    GenomeInfoDb,
    GenomicFeatures,
    GenomicRanges (>= 1.38.0),
    IRanges,
    Matrix,
    MatrixGenerics,
    methods,
    S4Vectors,
    stats,
    utils,
    VariantAnnotation
Suggests:
    biomaRt,
    BSgenome.Hsapiens.UCSC.hg38,
    BSgenome.Mmusculus.UCSC.mm10,
    BiocStyle,
    crisprBwa (>= 0.99.7),
    knitr,
    rmarkdown,
    Rbowtie,
    Rbwa,
    RCurl,
    testthat
biocViews:
    CRISPR,
    FunctionalGenomics,
    GeneTarget
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.2
VignetteBuilder: knitr
BugReports: https://github.com/Jfortin1/crisprDesign/issues
URL: https://github.com/Jfortin1/crisprDesign

bioc-issue-bot · 2022-05-12T17:42:56Z

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bioc-issue-bot · 2022-05-12T17:59:38Z

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bioc-issue-bot · 2022-05-12T21:59:59Z

Received a valid push on git.bioconductor.org; starting a build for commit id: e836d1c063f5f076e12946a001c810f6f22a8996

bioc-issue-bot · 2022-05-12T22:21:54Z

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bioc-issue-bot · 2022-05-24T00:16:07Z

Received a valid push on git.bioconductor.org; starting a build for commit id: ddc7277ceb65422f829bab2f7a1da7d452a3ba14

bioc-issue-bot · 2022-05-24T00:32:23Z

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Jfortin1 · 2022-06-10T17:55:43Z

@nturaga Thanks for reviewing one more of our CRISPR packages! Is there anything I should do from my side before you review the package?

nturaga · 2022-06-10T17:59:54Z

@Jfortin1 Just getting back into package reviews after the post-release work/conferences. Will get to it in the next week!

One thing you can do is fix the warning messages on build report before I have a look at it.

bioc-issue-bot · 2022-06-14T23:31:57Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 5773f9b78dba618a3b2e62734d4653e7c0901195

bioc-issue-bot · 2022-06-14T23:47:10Z

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bioc-issue-bot · 2022-06-15T03:58:50Z

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bioc-issue-bot · 2022-06-15T04:02:39Z

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bioc-issue-bot · 2022-06-15T04:16:04Z

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bioc-issue-bot · 2022-07-01T18:07:13Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 18399b976c9d74fb763006de96376d32579a0145

bioc-issue-bot · 2022-07-01T18:08:18Z

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nturaga · 2022-07-07T12:56:51Z

Hi @Jfortin1 , hope things are going well.

Review

DESCRIPTION

ok

NAMESPACE

ok

NEWS

ok

R

Well-written code! Some of the private functions could use a little
more documentation (consider this for a future time).
Remove some of the commented-out code.
The package is very extensive and took a long time to
review. There seems to be a new error on the build report (6 days
ago) caused by a namespace issue. Please investigate and fix it.

inst

ok

man

ok

tests

Very good!

vignettes

Good vignette.
Is there a reason you have a more_vignettes folder in the inst/
directory? You can just put additional vignettes in the vignettes/
dir.

bioc-issue-bot · 2022-07-07T16:34:01Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 0b95f8aa36d25eaa29bc22a04f614ffcfbea1bdf

bioc-issue-bot · 2022-07-07T16:43:22Z

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Jfortin1 · 2022-07-07T16:58:43Z

Thanks @nturaga for your review!
I've made the changes and the new push builds successfully.

Here are my answers to your review:

DESCRIPTION

ok

NAMESPACE

ok

NEWS

ok

R

Well-written code! Some of the private functions could use a little
more documentation (consider this for a future time).

JP: I agree; I went over all the R files and added comments on top of the private functions.

Remove some of the commented-out code.

JP: done.

The package is very extensive and took a long time to
review. There seems to be a new error on the build report (6 days
ago) caused by a namespace issue. Please investigate and fix it.

JP: fixed now.

inst

ok

man

ok

tests

Very good!

JP: thanks!

vignettes

Good vignette.

JP: thanks!

Is there a reason you have a more_vignettes folder in the inst/
directory? You can just put additional vignettes in the vignettes/
dir.

JP: deprecated now, I've removed it.

bioc-issue-bot · 2022-07-07T17:30:37Z

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

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reviewer, please see Reviewers Expectations.

Jfortin1 · 2022-07-16T15:09:57Z

@nturaga Hi Nitesh, the package is still not in the nightly build -- any chance we could add it in the next couple of days? Thanks!

lshep · 2022-07-16T20:51:33Z

I have been away on holiday and will be processing all the accepted packages on Monday. You can expect it in the daily builder on Tuesday

lshep · 2022-07-18T11:42:40Z

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Jfortin1 · 2022-07-18T18:03:01Z

@lshep Thank you!

bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Apr 26, 2022

vjcitn added the pre-check passed pre-review performed and ready to be added to git label May 12, 2022

bioc-issue-bot assigned nturaga May 12, 2022

bioc-issue-bot added the ERROR label May 12, 2022

bioc-issue-bot added WARNINGS and removed ERROR labels May 12, 2022

bioc-issue-bot added the ERROR label Jun 14, 2022

bioc-issue-bot removed the WARNINGS label Jun 15, 2022

bioc-issue-bot added the WARNINGS label Jun 15, 2022

bioc-issue-bot removed the WARNINGS label Jun 24, 2022

bioc-issue-bot added OK and removed ERROR labels Jun 24, 2022

bioc-issue-bot added ERROR and removed OK labels Jul 1, 2022

bioc-issue-bot added OK and removed ERROR labels Jul 7, 2022

nturaga added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels Jul 7, 2022

lshep closed this as completed Jul 18, 2022

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crisprDesign #2647

crisprDesign #2647

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nturaga commented Jul 7, 2022 •

edited

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Jfortin1 commented Jul 16, 2022

lshep commented Jul 16, 2022

lshep commented Jul 18, 2022

Jfortin1 commented Jul 18, 2022

crisprDesign #2647

crisprDesign #2647

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Jfortin1 commented Apr 26, 2022

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nturaga commented Jul 7, 2022 • edited

Review

DESCRIPTION

NAMESPACE

NEWS

R

inst

man

tests

vignettes

bioc-issue-bot commented Jul 7, 2022

bioc-issue-bot commented Jul 7, 2022

Jfortin1 commented Jul 7, 2022

DESCRIPTION

NAMESPACE

NEWS

R

inst

man

tests

vignettes

bioc-issue-bot commented Jul 7, 2022

Jfortin1 commented Jul 16, 2022

lshep commented Jul 16, 2022

lshep commented Jul 18, 2022

Jfortin1 commented Jul 18, 2022

nturaga commented Jul 7, 2022 •

edited