Merge branch 'master' into core-updates

1 files changed, 259 insertions, 0 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 09581d9fde..76ff773ef1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -23,6 +23,8 @@
   #:use-module (guix download)
   #:use-module (guix build-system r)
   #:use-module (gnu packages)
+  #:use-module (gnu packages cran)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages bioinformatics))
 
@@ -70,3 +72,260 @@ the Human Protein Atlas project.")
 customizable permutation tests to assess the association between genomic
 region sets and other genomic features.")
     (license license:artistic2.0)))
+
+(define-public r-diffbind
+  (package
+    (name "r-diffbind")
+    (version "2.6.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DiffBind" version))
+       (sha256
+        (base32
+         "1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp"))))
+    (properties `((upstream-name . "DiffBind")))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-amap" ,r-amap)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-deseq2" ,r-deseq2)
+       ("r-dplyr" ,r-dplyr)
+       ("r-edger" ,r-edger)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-gplots" ,r-gplots)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-limma" ,r-limma)
+       ("r-locfit" ,r-locfit)
+       ("r-rcolorbrewer" , r-rcolorbrewer)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-systempiper" ,r-systempiper)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "http://bioconductor.org/packages/DiffBind")
+    (synopsis "Differential binding analysis of ChIP-Seq peak data")
+    (description
+     "This package computes differentially bound sites from multiple
+ChIP-seq experiments using affinity (quantitative) data.  Also enables
+occupancy (overlap) analysis and plotting functions.")
+    (license license:artistic2.0)))
+
+(define-public r-ripseeker
+  (package
+    (name "r-ripseeker")
+    (version "1.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RIPSeeker" version))
+       (sha256
+        (base32
+         "0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y"))))
+    (properties `((upstream-name . "RIPSeeker")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-s4vectors" ,r-s4vectors)
+       ("r-iranges" ,r-iranges)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-rtracklayer" ,r-rtracklayer)))
+    (home-page "http://bioconductor.org/packages/RIPSeeker")
+    (synopsis
+     "Identifying protein-associated transcripts from RIP-seq experiments")
+    (description
+     "This package infers and discriminates RIP peaks from RIP-seq alignments
+using two-state HMM with negative binomial emission probability.  While
+RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
+a suite of bioinformatics tools integrated within this self-contained software
+package comprehensively addressing issues ranging from post-alignments
+processing to visualization and annotation.")
+    (license license:gpl2)))
+
+(define-public r-multtest
+  (package
+    (name "r-multtest")
+    (version "2.34.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "multtest" version))
+       (sha256
+        (base32
+         "0n11rd49xl2vn3ldmfips7d3yb70l8npjcqsxyswr9ypjhgzkv9j"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-survival" ,r-survival)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biobase" ,r-biobase)
+       ("r-mass" ,r-mass)))
+    (home-page "http://bioconductor.org/packages/multtest")
+    (synopsis "Resampling-based multiple hypothesis testing")
+    (description
+     "This package can do non-parametric bootstrap and permutation
+resampling-based multiple testing procedures (including empirical Bayes
+methods) for controlling the family-wise error rate (FWER), generalized
+family-wise error rate (gFWER), tail probability of the proportion of
+false positives (TPPFP), and false discovery rate (FDR).  Several choices
+of bootstrap-based null distribution are implemented (centered, centered
+and scaled, quantile-transformed).  Single-step and step-wise methods are
+available.  Tests based on a variety of T- and F-statistics (including
+T-statistics based on regression parameters from linear and survival models
+as well as those based on correlation parameters) are included.  When probing
+hypotheses with T-statistics, users may also select a potentially faster null
+distribution which is multivariate normal with mean zero and variance
+covariance matrix derived from the vector influence function.  Results are
+reported in terms of adjusted P-values, confidence regions and test statistic
+cutoffs.  The procedures are directly applicable to identifying differentially
+expressed genes in DNA microarray experiments.")
+    (license license:lgpl3)))
+
+(define-public r-chippeakanno
+  (package
+    (name "r-chippeakanno")
+    (version "3.12.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ChIPpeakAnno" version))
+       (sha256
+        (base32
+         "1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04"))))
+    (properties `((upstream-name . "ChIPpeakAnno")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-go-db" ,r-go-db)
+       ("r-biomart" ,r-biomart)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-annotationdbi" ,r-annotationdbi)
+       ("r-limma" ,r-limma)
+       ("r-multtest" ,r-multtest)
+       ("r-rbgl" ,r-rbgl)
+       ("r-graph" ,r-graph)
+       ("r-biocinstaller" ,r-biocinstaller)
+       ("r-regioner" ,r-regioner)
+       ("r-dbi" ,r-dbi)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-biobase" ,r-biobase)
+       ("r-seqinr" ,r-seqinr)
+       ("r-idr" ,r-idr)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-venndiagram" ,r-venndiagram)))
+    (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
+    (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
+    (description
+     "The package includes functions to retrieve the sequences around the peak,
+obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
+custom features such as most conserved elements and other transcription factor
+binding sites supplied by users.  Starting 2.0.5, new functions have been added
+for finding the peaks with bi-directional promoters with summary statistics
+(peaksNearBDP), for summarizing the occurrence of motifs in peaks
+(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
+enrichedGO (addGeneIDs).")
+    (license license:gpl2+)))
+
+(define-public r-marray
+  (package
+    (name "r-marray")
+    (version "1.56.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "marray" version))
+              (sha256
+               (base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-limma" ,r-limma)))
+    (home-page "http://bioconductor.org/packages/marray")
+    (synopsis "Exploratory analysis for two-color spotted microarray data")
+    (description "This package contains class definitions for two-color spotted
+microarray data.  It also includes fuctions for data input, diagnostic plots,
+normalization and quality checking.")
+    (license license:lgpl2.0+)))
+
+(define-public r-cghbase
+  (package
+   (name "r-cghbase")
+   (version "1.38.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "CGHbase" version))
+            (sha256
+             (base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm"))))
+   (properties `((upstream-name . "CGHbase")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-biobase" ,r-biobase)
+      ("r-marray" ,r-marray)))
+   (home-page "http://bioconductor.org/packages/CGHbase")
+   (synopsis "Base functions and classes for arrayCGH data analysis")
+   (description "This package contains functions and classes that are needed by
+the @code{arrayCGH} packages.")
+   (license license:gpl2+)))
+
+(define-public r-cghcall
+  (package
+   (name "r-cghcall")
+   (version "2.40.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "CGHcall" version))
+            (sha256
+             (base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch"))))
+   (properties `((upstream-name . "CGHcall")))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-biobase" ,r-biobase)
+      ("r-cghbase" ,r-cghbase)
+      ("r-impute" ,r-impute)
+      ("r-dnacopy" ,r-dnacopy)
+      ("r-snowfall" ,r-snowfall)))
+   (home-page "http://bioconductor.org/packages/CGHcall")
+   (synopsis "Base functions and classes for arrayCGH data analysis")
+   (description "This package contains functions and classes that are needed by
+@code{arrayCGH} packages.")
+   (license license:gpl2+)))
+
+(define-public r-qdnaseq
+  (package
+    (name "r-qdnaseq")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "QDNAseq" version))
+              (sha256
+               (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy"))))
+    (properties `((upstream-name . "QDNAseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-cghbase" ,r-cghbase)
+       ("r-cghcall" ,r-cghcall)
+       ("r-dnacopy" ,r-dnacopy)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-r-utils" ,r-r-utils)
+       ("r-rsamtools" ,r-rsamtools)))
+    (home-page "http://bioconductor.org/packages/QDNAseq")
+    (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
+    (description "The genome is divided into non-overlapping fixed-sized bins,
+number of sequence reads in each counted, adjusted with a simultaneous
+two-dimensional loess correction for sequence mappability and GC content, and
+filtered to remove spurious regions in the genome.  Downstream steps of
+segmentation and calling are also implemented via packages DNAcopy and CGHcall,
+respectively.")
+    (license license:gpl2+)))