Re: [PATCH] gnu: Add r-sva
Rawrites: > follows the patch with the reduced description, sorry for the long version. > I do not know why you get the "corrupt" message, I hope that attaching the > patch file could solve the issue. The inline patch didn’t work, but the attached version was fine. Don’t know what went wrong here. Thanks for your patience! I made a few minor changes: * added a trailing period to the commit summary line * converted the description to use two spaced between sentences * slightly reworded the second sentence Thanks again for the patch! I pushed it to master as dd42a330d. I’m looking forward to more of your contributions to the statistics and bioinformatics modules! -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC http://elephly.net
Re: [PATCH] gnu: Add r-sva
Hi Ricardo, On Fri, Jan 13, 2017 at 10:52 PM Ricardo Wurmuswrote: > Ra writes: > > > * gnu/packages/bioinformatics.scm (r-sva): New variable. > > --- > > gnu/packages/bioinformatics.scm | 35 +++ > > 1 file changed, 35 insertions(+) > > Thanks for the patch. I tried to apply this but got this error: > > error: corrupt patch at line 12 > > Could you resend the patch please? > > > +(description > > + "This package contains functions for removing batch effects and > > +other unwanted variation in high-throughput experiment. Specifically, > > +the sva package contains functions for the identifying and building > > +surrogate variables for high-dimensional data sets. Surrogate variables > > +are covariates constructed directly from high-dimensional data (like > gene > > +expression/RNA sequencing/methylation/brain imaging data) that can be > used > > +in subsequent analyses to adjust for unknown, unmodeled, or latent > sources > > +of noise. The sva package can be used to remove artifacts in three ways: > > +1. identifying and estimating surrogate variables for unknown sources of > > +variation in high-throughput experiments Leek and Storey 2007 PLoS > > Genetics, > > + 2008 PNAS,2. directly removing known batch effects using ComBat > > +Johnson et al. 2007 Biostatistics and 3. removing batch effects with > known > > +control probes Leek 2014 biorXiv. Removing batch effects and using > > surrogate > > +variables in differential expression analysis have been shown to reduce > > +dependence, stabilize error rate estimates, and improve reproducibility, > > +see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 > Nat. > > Reviews Genetics.") > > +(license license:artistic2.0))) > > Could you please shorten the description? A paragraph or two would be > sufficient. We also don’t need the references to publications. If you > decide to keep (a shortened variant of) the enumeration, please use > texinfo syntax. > > follows the patch with the reduced description, sorry for the long version. I do not know why you get the "corrupt" message, I hope that attaching the patch file could solve the issue. * gnu/packages/bioinformatics.scm (r-sva): New variable. --- gnu/packages/bioinformatics.scm | 26 ++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d82b6c0..867a72e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7995,3 +7995,29 @@ immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.") (license license:gpl2))) + +(define-public r-sva + (package +(name "r-sva") +(version "3.22.0") +(source + (origin + (method url-fetch) + (uri (bioconductor-uri "sva" version)) + (sha256 +(base32 + "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn" +(build-system r-build-system) +(propagated-inputs + `(("r-genefilter" ,r-genefilter))) +(home-page "http://bioconductor.org/packages/sva;) +(synopsis "Surrogate variable analysis") +(description + "This package contains functions for removing batch effects and +other unwanted variation in high-throughput experiment. The package +contains functions for identifying and building surrogate variables +for high-dimensional data sets. Surrogate variables are covariates +constructed directly from high-dimensional data like gene expression/RNA +sequencing/methylation/brain imaging data that can be used in subsequent +analyses to adjust for unknown, unmodeled, or latent sources of noise.") +(license license:artistic2.0))) -- 1.9.1 0001-gnu-Add-r-sva.patch Description: Binary data
Re: [PATCH] gnu: Add r-sva
Rawrites: > * gnu/packages/bioinformatics.scm (r-sva): New variable. > --- > gnu/packages/bioinformatics.scm | 35 +++ > 1 file changed, 35 insertions(+) Thanks for the patch. I tried to apply this but got this error: error: corrupt patch at line 12 Could you resend the patch please? > +(description > + "This package contains functions for removing batch effects and > +other unwanted variation in high-throughput experiment. Specifically, > +the sva package contains functions for the identifying and building > +surrogate variables for high-dimensional data sets. Surrogate variables > +are covariates constructed directly from high-dimensional data (like gene > +expression/RNA sequencing/methylation/brain imaging data) that can be used > +in subsequent analyses to adjust for unknown, unmodeled, or latent sources > +of noise. The sva package can be used to remove artifacts in three ways: > +1. identifying and estimating surrogate variables for unknown sources of > +variation in high-throughput experiments Leek and Storey 2007 PLoS > Genetics, > + 2008 PNAS,2. directly removing known batch effects using ComBat > +Johnson et al. 2007 Biostatistics and 3. removing batch effects with known > +control probes Leek 2014 biorXiv. Removing batch effects and using > surrogate > +variables in differential expression analysis have been shown to reduce > +dependence, stabilize error rate estimates, and improve reproducibility, > +see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. > Reviews Genetics.") > +(license license:artistic2.0))) Could you please shorten the description? A paragraph or two would be sufficient. We also don’t need the references to publications. If you decide to keep (a shortened variant of) the enumeration, please use texinfo syntax. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC http://elephly.net
[PATCH] gnu: Add r-sva
* gnu/packages/bioinformatics.scm (r-sva): New variable. --- gnu/packages/bioinformatics.scm | 35 +++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d82b6c0..c6acab1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7995,3 +7995,38 @@ immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.") (license license:gpl2))) + +(define-public r-sva + (package +(name "r-sva") +(version "3.22.0") +(source + (origin + (method url-fetch) + (uri (bioconductor-uri "sva" version)) + (sha265 +(base32 + "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn" +(build-system r-build-system) +(propagated-inputs + `(("r-genefilter" ,r-genefilter))) +(home-page "http://bioconductor.org/packages/sva;) +(synopsis "Surrogate variable analysis") +(description + "This package contains functions for removing batch effects and +other unwanted variation in high-throughput experiment. Specifically, +the sva package contains functions for the identifying and building +surrogate variables for high-dimensional data sets. Surrogate variables +are covariates constructed directly from high-dimensional data (like gene +expression/RNA sequencing/methylation/brain imaging data) that can be used +in subsequent analyses to adjust for unknown, unmodeled, or latent sources +of noise. The sva package can be used to remove artifacts in three ways: +1. identifying and estimating surrogate variables for unknown sources of +variation in high-throughput experiments Leek and Storey 2007 PLoS Genetics, + 2008 PNAS,2. directly removing known batch effects using ComBat +Johnson et al. 2007 Biostatistics and 3. removing batch effects with known +control probes Leek 2014 biorXiv. Removing batch effects and using surrogate +variables in differential expression analysis have been shown to reduce +dependence, stabilize error rate estimates, and improve reproducibility, +see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics.") +(license license:artistic2.0))) -- 1.9.1 0001-gnu-Add-r-sva.patch Description: Binary data