From: Ra <ilpuccio.febo@gmail.com>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: guix-devel <guix-devel@gnu.org>
Subject: Re: [PATCH] Add r-scran 1.2.0 and all its dependencies
Date: Wed, 28 Dec 2016 09:26:52 +0000 [thread overview]
Message-ID: <CACQsWTNw1aaGRhb6kn8g1Z-2y6O_VQzgE1yYy0btS+OPGj7T_Q@mail.gmail.com> (raw)
In-Reply-To: <CACQsWTPNpwq-gj8Sf-RqPCSL-a=QBSEz244h=T6Tvs_U3mK1Wg@mail.gmail.com>
[-- Attachment #1.1: Type: text/plain, Size: 1222 bytes --]
Hi Ricardo,
there was an issue with the r-shiny patch, the license was wrong. So this
is the new set of patches.
On Tue, Dec 27, 2016 at 10:25 PM Ra <ilpuccio.febo@gmail.com> wrote:
> Dear Ricardo,
> I try to satisfy all the requirements. What do you think ?
> In attachment the patches.
>
> Shiny now is in web.scm
>
> I reformat the description and fixed the synopsis. I also re checked the
> licenses.
> I have created a single patch for each r-package.
>
> --
> Raoul
>
>
>
> On Tue, Dec 27, 2016 at 6:06 PM Ra <ilpuccio.febo@gmail.com> wrote:
>
> On Tue, Dec 27, 2016 at 6:00 PM Ricardo Wurmus <rekado@elephly.net> wrote:
>
>
> Ra <ilpuccio.febo@gmail.com> writes:
>
> > guix import cran --archive=bioconductor scater
> >
> > I had to add the missing dependencies by hand, is there a recursive way
> to do so?
>
> Yes, you can just pass “--recursive” or “-r” and the importer will spit
> out package expressions for all unpackaged dependencies. A current
> limitation is that it doesn’t cross over from Bioconductor to CRAN.
>
> Nice, I will try
>
>
>
> --
> Ricardo
>
> GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
> http://elephly.net
>
>
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[-- Attachment #2: 0006-gnu-Add-r-shiny.patch --]
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From bb3c01e940be4c4357591aa066b9ffc65371615c Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Wed, 28 Dec 2016 10:11:45 +0100
Subject: [PATCH 06/11] gnu: Add r-shiny.
---
gnu/packages/web.scm | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 07c4c0d..cec659e 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3968,3 +3968,32 @@ useful for users behind restrictive firewalls. As long as Web traffic is
allowed, even through a HTTP-only proxy, httptunnel can be combined with other
tools like SSH (Secure Shell) to reach the outside world.")
(license l:gpl2+)))
+
+(define-public r-shiny
+ (package
+ (name "r-shiny")
+ (version "0.14.2")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "shiny" version))
+ (sha256
+ (base32
+ "1sx8c490hbj7lsmvwwq5p4a32dcz4fp4wp1zvaaf2pfg713pk593"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-digest" ,r-digest)
+ ("r-htmltools" ,r-htmltools)
+ ("r-httpuv" ,r-httpuv)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-mime" ,r-mime)
+ ("r-r6" ,r-r6)
+ ("r-sourcetools" ,r-sourcetools)
+ ("r-xtable" ,r-xtable)))
+ (home-page "http://shiny.rstudio.com")
+ (synopsis "Web application framework for R")
+ (description
+ "Makes it incredibly easy to build interactive web applications with R.
+Automatic reactive binding between inputs and outputs and extensive pre-built
+widgets make it possible to build beautiful, responsive, and powerful
+applications with minimal effort.")
+ (license l:gpl3)))
--
1.9.1
[-- Attachment #3: 0005-gnu-Add-r-statmod.patch --]
[-- Type: application/octet-stream, Size: 1746 bytes --]
From a9b2d5a94ea4c2560611e46b523f57d091abab3c Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 21:58:05 +0100
Subject: [PATCH 05/11] gnu: Add r-statmod.
---
gnu/packages/statistics.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index fd77ef8..36061b1 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3897,3 +3897,28 @@ tokenized representation of R code.")
the arrangement of points within a category reflects the density of data
at that region, and avoids over-plotting.")
(license license:gpl2+)))
+
+(define-public r-statmod
+ (package
+ (name "r-statmod")
+ (version "1.4.27")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "statmod" version))
+ (sha256
+ (base32
+ "14yilq9d3z20hig4rs8bjqyydw3dfx90mhmzvw9w8p16h0s595sn"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/statmod")
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (synopsis "Statistical modeling")
+ (description
+ "This package provides a collection of algorithms and functions to aid
+statistical modeling. Includes growth curve comparisons, limiting dilution
+analysis (aka ELDA), mixed linear models, heteroscedastic regression,
+inverse-Gaussian probability calculations, Gauss quadrature and a secure
+convergence algorithm for nonlinear models. Includes advanced generalized
+linear model functions that implement secure convergence, dispersion modeling
+and Tweedie power-law families.")
+ (license license:gpl3)))
--
1.9.1
[-- Attachment #4: 0010-gnu-Add-r-scater.patch --]
[-- Type: application/octet-stream, Size: 2064 bytes --]
From 14222e8cdbfc49093172d9f1a3bcc7999e72bcb5 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:16:33 +0100
Subject: [PATCH 10/11] gnu: Add r-scater.
---
gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 154f509..678fae7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7685,6 +7685,44 @@ and for letting R applications work on datasets that are larger than the
available RAM.")
(license license:artistic2.0)))
+(define-public r-scater
+ (package
+ (name "r-scater")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scater" version))
+ (sha256
+ (base32
+ "0pambafir3aqpgk7kdq5i2pn0278d97bn2qb9712c0jivw363whf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biomart" ,r-biomart)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-edger" ,r-edger)
+ ("r-ggbeeswarm" ,r-ggbeeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-limma" ,r-limma)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-plyr" ,r-plyr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rhdf5" ,r-rhdf5)
+ ("r-rjson" ,r-rjson)
+ ("r-shiny" ,r-shiny)
+ ("r-shinydashboard" ,r-shinydashboard)
+ ("r-tximport" ,r-tximport)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://github.com/davismcc/scater")
+ (synopsis "Single-cell analysis toolkit for gene expression data in R")
+ (description
+ "This package provides a collection of tools for doing various analyses
+of single-cell RNA-seq gene expression data, with a focus on quality control.")
+ (license license:gpl2+)))
+
+
(define-public emboss
(package
(name "emboss")
--
1.9.1
[-- Attachment #5: 0008-gnu-Add-r-tximport.patch --]
[-- Type: application/octet-stream, Size: 1689 bytes --]
From e6855970c278627a0ebbbe557c054bac653c513c Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:11:28 +0100
Subject: [PATCH 08/11] gnu: Add r-tximport.
---
gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d423f08..dbe1b92 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7618,6 +7618,27 @@ for DNA and protein sequences. This package supports several sequence
kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
(license license:gpl2+)))
+(define-public r-tximport
+ (package
+ (name "r-tximport")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "tximport" version))
+ (sha256
+ (base32
+ "1k5a7dad6zqg936s17f6cmwgqp11x24z9zhxndsgwbscgpyhpcb0"))))
+ (build-system r-build-system)
+ (home-page "http://bioconductor.org/packages/tximport")
+ (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
+ (description
+ "Imports transcript-level abundance, estimated counts and transcript
+lengths, and summarizes into matrices for use with downstream gene-level
+analysis packages. Average transcript length, weighted by sample-specific
+transcript abundance estimates, is provided as a matrix which can be used
+as an offset for different expression of gene-level counts.")
+ (license license:gpl2)))
+
(define-public emboss
(package
(name "emboss")
--
1.9.1
[-- Attachment #6: 0003-gnu-Add-r-sourcetools.patch --]
[-- Type: application/octet-stream, Size: 1469 bytes --]
From 6821f41f9bf79b853724eb1fd5f01d7acba5fe5a Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 20:52:20 +0100
Subject: [PATCH 03/11] gnu: Add r-sourcetools.
---
gnu/packages/statistics.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b406e9e..4440565 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3852,3 +3852,25 @@ density using quasirandom noise.")
"The bee swarm plot is a one-dimensional scatter plot like stripchart,
but with closely-packed, non-overlapping points.")
(license license:artistic2.0)))
+
+(define-public r-sourcetools
+ (package
+ (name "r-sourcetools")
+ (version "0.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sourcetools" version))
+ (sha256
+ (base32
+ "0jx6kslygfqaic3cmjwag3dy98q1a2dw20cz7z8agsknmmbk6dy2"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/sourcetools")
+ (synopsis
+ "Tools for reading, tokenizing and parsing R code.")
+ (description
+ "Tools for the reading and tokenization of R code. The
+sourcetools package provides both an R and C++ interface for the
+tokenization of R code, and helpers for interacting with the
+tokenized representation of R code.")
+ (license license:expat)))
--
1.9.1
[-- Attachment #7: 0001-gnu-Add-r-vipor.patch --]
[-- Type: application/octet-stream, Size: 1441 bytes --]
From 40318a6d2d4f6ca1c5539dfe21c63b503ca00aea Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 20:35:41 +0100
Subject: [PATCH 01/11] gnu: Add r-vipor.
---
gnu/packages/statistics.scm | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f868da2..f30e8e9 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3815,3 +3815,22 @@ with alternating row colors) in LaTeX and HTML formats easily from
@code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
@code{cbind.mytable} objects.")
(license license:gpl2+)))
+
+(define-public r-vipor
+ (package
+ (name "r-vipor")
+ (version "0.4.4")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "vipor" version))
+ (sha256
+ (base32
+ "0p1z9a3fazl78pj8a1i2n62v8hrs8cinq82j9wpawhmfkn3dggss"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/vipor")
+ (synopsis "Plot categorical data using quasirandom noise and density estimates")
+ (description
+ "Generate a violin point plot, a combination of a violin/histogram plot
+and a scatter plot by offsetting points within a category based on their
+density using quasirandom noise.")
+ (license license:gpl2+)))
--
1.9.1
[-- Attachment #8: 0002-gnu-Add-r-beeswarm.patch --]
[-- Type: application/octet-stream, Size: 1376 bytes --]
From b5b9ae7e2386c8ddb8f86f8b9edad0d000f34928 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 20:46:47 +0100
Subject: [PATCH 02/11] gnu: Add r-beeswarm.
---
gnu/packages/statistics.scm | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f30e8e9..b406e9e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3834,3 +3834,21 @@ with alternating row colors) in LaTeX and HTML formats easily from
and a scatter plot by offsetting points within a category based on their
density using quasirandom noise.")
(license license:gpl2+)))
+
+(define-public r-beeswarm
+ (package
+ (name "r-beeswarm")
+ (version "0.2.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "beeswarm" version))
+ (sha256
+ (base32
+ "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
+ (build-system r-build-system)
+ (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
+ (synopsis "The beeswarm plot, an alternative to stripchart")
+ (description
+ "The bee swarm plot is a one-dimensional scatter plot like stripchart,
+but with closely-packed, non-overlapping points.")
+ (license license:artistic2.0)))
--
1.9.1
[-- Attachment #9: 0007-gnu-Add-r-shinydashboard.patch --]
[-- Type: application/octet-stream, Size: 1437 bytes --]
From 7b4704fcc4bdf455522c045002e88d875e050e16 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Wed, 28 Dec 2016 10:15:48 +0100
Subject: [PATCH 07/11] gnu: Add r-shinydashboard.
---
gnu/packages/web.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index cec659e..724abd1 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3997,3 +3997,24 @@ Automatic reactive binding between inputs and outputs and extensive pre-built
widgets make it possible to build beautiful, responsive, and powerful
applications with minimal effort.")
(license l:gpl3)))
+
+(define-public r-shinydashboard
+ (package
+ (name "r-shinydashboard")
+ (version "0.5.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "shinydashboard" version))
+ (sha256
+ (base32
+ "0anw22qxbis69zm0ls6alsc3ann27hvgs5mv1wvr4ppk7q8cg4l2"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-htmltools" ,r-htmltools)
+ ("r-shiny" ,r-shiny)))
+ (home-page "http://rstudio.github.io/shinydashboard/")
+ (synopsis "Create dashboards with shiny")
+ (description
+ "Create dashboards with shiny. This package provides a theme on top of
+Shiny, making it easy to create attractive dashboards.")
+ (license l:gpl2)))
--
1.9.1
[-- Attachment #10: 0004-gnu-Add-r-ggbeeswarm.patch --]
[-- Type: application/octet-stream, Size: 1552 bytes --]
From e96e737470adbd7cf39c7308b2125b6724c3d3ea Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 21:52:04 +0100
Subject: [PATCH 04/11] gnu: Add r-ggbeeswarm.
---
gnu/packages/statistics.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 4440565..fd77ef8 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3874,3 +3874,26 @@ sourcetools package provides both an R and C++ interface for the
tokenization of R code, and helpers for interacting with the
tokenized representation of R code.")
(license license:expat)))
+
+(define-public r-ggbeeswarm
+ (package
+ (name "r-ggbeeswarm")
+ (version "0.5.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "ggbeeswarm" version))
+ (sha256
+ (base32
+ "1jgp55rvmzc4agcrlsjn8m5lk85di9c4wj94xzikqkql4lvq3qpd"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beeswarm" ,r-beeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-vipor" ,r-vipor)))
+ (home-page "https://github.com/eclarke/ggbeeswarm")
+ (synopsis "Categorical scatter (violin point) plots")
+ (description
+ "Provides two methods of plotting categorical scatter plots such that
+the arrangement of points within a category reflects the density of data
+at that region, and avoids over-plotting.")
+ (license license:gpl2+)))
--
1.9.1
[-- Attachment #11: 0009-gnu-Add-r-rhdf5.patch --]
[-- Type: application/octet-stream, Size: 2736 bytes --]
From 922c7db2c1e4e9f9f8e1a9795686ada137d2fc7f Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:14:28 +0100
Subject: [PATCH 09/11] gnu: Add r-rhdf5.
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dbe1b92..154f509 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7639,6 +7639,52 @@ transcript abundance estimates, is provided as a matrix which can be used
as an offset for different expression of gene-level counts.")
(license license:gpl2)))
+(define-public r-rhdf5
+ (package
+ (name "r-rhdf5")
+ (version "2.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rhdf5" version))
+ (sha256
+ (base32
+ "0pb04li55ysag30s7rap7nnivc0rqmgsmpj43kin0rxdabfn1w0k"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unpack-smallhdf5
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* (
+ (out (assoc-ref %outputs "out"))
+ (name "src/hdf5source/hdf5small.tgz")
+ (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")))
+ (begin
+ (system* tar "-xzvf" name "-C" "src/" )
+ (substitute* "src/Makevars"
+ (("^.*cd hdf5source &&.*$") "")
+ (("^.*gunzip -dc hdf5small.tgz.*$") "")
+ (("^.*rm -rf hdf5.*$") "")
+ (("^.*mv hdf5source/hdf5 ..*$") ""))
+ (substitute* "src/hdf5/configure"
+ (("/bin/mv") "mv")))))))))
+ (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("tar" ,tar)
+ ("perl" ,perl)
+ ("zlib" ,zlib)))
+ (home-page "http://bioconductor.org/packages/rhdf5")
+ (synopsis "HDF5 interface to R")
+ (description
+ "This R/Bioconductor package provides an interface between HDF5 and R.
+HDF5's main features are the ability to store and access very large and/or
+complex datasets and a wide variety of metadata on mass storage (disk) through
+a completely portable file format. The rhdf5 package is thus suited for the
+exchange of large and/or complex datasets between R and other software package,
+and for letting R applications work on datasets that are larger than the
+available RAM.")
+ (license license:artistic2.0)))
+
(define-public emboss
(package
(name "emboss")
--
1.9.1
[-- Attachment #12: 0011-gnu-Add-r-scran.patch --]
[-- Type: application/octet-stream, Size: 1811 bytes --]
From 187f678cdc529b7c6d1cf11931866394a427dfd3 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 22:18:32 +0100
Subject: [PATCH 11/11] gnu: Add r-scran.
---
gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 678fae7..5e06664 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7722,6 +7722,35 @@ available RAM.")
of single-cell RNA-seq gene expression data, with a focus on quality control.")
(license license:gpl2+)))
+(define-public r-scran
+ (package
+ (name "r-scran")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scran" version))
+ (sha256
+ (base32
+ "1wnsmp46x9zgbiacf9hxhpy42gxbvwf8q2x6dchc3r9g4p2s65c5"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-dynamictreecut" ,r-dynamictreecut)
+ ("r-edger" ,r-edger)
+ ("r-scater" ,r-scater)
+ ("r-shiny" ,r-shiny)
+ ("r-statmod" ,r-statmod)
+ ("r-zoo" ,r-zoo)))
+ (home-page "http://bioconductor.org/packages/scran")
+ (synopsis "Methods for single-cell RNA-Seq data analysis")
+ (description
+ "Implements a variety of low-level analyses of single-cell RNA-seq data.
+Methods are provided for normalization of cell-specific biases, assignment of
+cell cycle phase, and detection of highly variable and significantly
+correlated genes.")
+ (license license:gpl3)))
(define-public emboss
(package
--
1.9.1
next prev parent reply other threads:[~2016-12-28 9:27 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-12-27 9:14 [PATCH] Add r-scran 1.2.0 and all its dependencies Ra
2016-12-27 16:02 ` Ricardo Wurmus
2016-12-27 16:34 ` Ra
2016-12-27 16:59 ` Ricardo Wurmus
2016-12-27 17:06 ` Ra
2016-12-27 21:25 ` Ra
2016-12-28 9:26 ` Ra [this message]
2016-12-29 21:52 ` Ricardo Wurmus
2017-01-31 21:47 ` Ricardo Wurmus
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