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doubletrouble
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- Repository: https://github.com/almeidasilvaf/doubletrouble
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Hi @almeidasilvaf
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: doubletrouble
Title: Identification and classification of duplicated genes
Version: 0.99.0
Date: 2022-05-29
Authors@R:
c(
person(given = "Fabrício",
family = "Almeida-Silva",
role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-5314-2964")),
person(given = "Yves",
family = "Van de Peer",
role = "aut",
email = "[email protected]",
comment = c(ORCID = "0000-0003-4327-3730"))
)
Description: doubletrouble aims to identify duplicated genes from
whole-genome protein sequences and classify them based on their modes
of duplication. The duplication modes are:
i. whole-genome duplication (WGD);
ii. tandem duplication (TD);
iii. proximal duplication (PD);
iv. transposed duplication (TRD) and;
v. dispersed duplication (DD).
If users want a simpler classification scheme, duplicates can also be
classified into WGD- and SSD-derived (small-scale duplication) gene pairs.
Besides classifying gene pairs, users can also classify genes, so that
each gene is assigned a unique mode of duplication.
Users can also calculate substitution rates per substitution site (i.e., Ka
and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian
Mixture Models (GMMs), and classify gene pairs into age groups based on Ks
peaks.
License: GPL-3
URL: https://github.com/almeidasilvaf/doubletrouble
BugReports: https://support.bioconductor.org/t/doubletrouble
biocViews:
Software,
WholeGenome,
ComparativeGenomics,
FunctionalGenomics,
Phylogenetics,
Network
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
Imports:
syntenet,
GenomicRanges,
Biostrings,
mclust,
MSA2dist (>= 1.1.5),
ggplot2,
stats,
utils
Depends:
R (>= 4.2.0)
Suggests:
testthat (>= 3.0.0),
knitr,
feature,
BiocStyle,
rmarkdown,
covr,
sessioninfo
Config/testthat/edition: 3
VignetteBuilder: knitr
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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.
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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Thanks @almeidasilvaf, this was extremely pleasurable to review. The code was nicely written and the vignette was clear. There are plenty of tests and examples.
- [ ] The only thing I think worth changing is when you use the colon operator
1:2, can easily be replaced byc(1, 2)and is much easier to read. For longer regular sequances is safer to use the appropriateseq.
Received a valid push on git.bioconductor.org; starting a build for commit id: ce28f43ed9e5f4accf90a10751dc54d2777235dc
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
[email protected]:packages/doubletrouble to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi, @ococrook
Thank you very much for your feedback!
- [x] The only thing I think worth changing is when you use the colon operator 1:2, can easily be replaced by c(1, 2) and is much easier to read. For longer regular sequances is safer to use the appropriate seq.
Agreed. I replaced m:n with c(m, n) or seq(m, n, by = 1) throughout.
Best, Fabricio
Thanks Fabricio, I'm happy to accept the package after a tiny fix. Could you update the NEWS.md file so it matches the Desciption file?
Received a valid push on git.bioconductor.org; starting a build for commit id: 0d8851d97675e5d7c12c7b52144e58af9c5d5b1b
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
[email protected]:packages/doubletrouble to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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