Closed Jfortin1 closed 2 years ago
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
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Dear Package contributor,
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Received a valid push on git.bioconductor.org; starting a build for commit id: e836d1c063f5f076e12946a001c810f6f22a8996
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Received a valid push on git.bioconductor.org; starting a build for commit id: ddc7277ceb65422f829bab2f7a1da7d452a3ba14
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@nturaga Thanks for reviewing one more of our CRISPR packages! Is there anything I should do from my side before you review the package?
@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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 5773f9b78dba618a3b2e62734d4653e7c0901195
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Received a valid push on git.bioconductor.org; starting a build for commit id: 56b7da07c773e1f5955c76ee434c19f4a0d5bc89
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Received a valid push on git.bioconductor.org; starting a build for commit id: 9bcb4635707ff9054b9adf0b9b101e8307312a5a
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Received a valid push on git.bioconductor.org; starting a build for commit id: bea287ede55edf49d3d3543aba19d0852d0eca22
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Your package has been built on Linux, Mac, and Windows.
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Hi @Jfortin1 , hope things are going well.
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.
ok
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 0b95f8aa36d25eaa29bc22a04f614ffcfbea1bdf
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Your package has been built on Linux, Mac, and Windows.
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Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
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Thanks @nturaga for your review! I've made the changes and the new push builds successfully.
Here are my answers to your review:
ok
ok
ok
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.
ok
ok
Very good!
JP: thanks!
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.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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@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!
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
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@lshep Thank you!
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