From 65050163e01d40d197f57748dc82072026676445 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 13:42:00 +0200 Subject: gnu: r-chippeakanno: Update to 3.14.1. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7e993189d6..1ff86779e8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -363,14 +363,14 @@ expressed genes in DNA microarray experiments.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.14.0") + (version "3.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0")))) + "1cn1hfc3nvsf2n3563lkmvwjxfbiygx7f84zk683p89gy7zi1gyj")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5dfe491290b14a1ee7efd70f9cd083969c24e1c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:46:12 +0200 Subject: gnu: r-graph: Move from bioinformatics to bioconductor. * gnu/packages/bioinformatics.scm (r-graph): Move from here... * gnu/packages/bioconductor.scm (r-graph): ...to here. --- gnu/packages/bioconductor.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1ff86779e8..fc01c2283b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -360,6 +360,25 @@ cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.") (license license:lgpl3))) +(define-public r-graph + (package + (name "r-graph") + (version "1.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "graph" version)) + (sha256 + (base32 + "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/graph") + (synopsis "Handle graph data structures in R") + (description + "This package implements some simple graph handling capabilities for R.") + (license license:artistic2.0))) + (define-public r-chippeakanno (package (name "r-chippeakanno") -- cgit v1.2.3 From a207bca2adf5371aabe41f28203c0e3e7bfbacad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 5 Sep 2018 19:47:19 +0200 Subject: gnu: r-codedepends: Move from cran to bioconductor. * gnu/packages/cran.scm (r-codedepends): Move from here... * gnu/packages/bioconductor.scm (r-codedepends): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fc01c2283b..a47a5aad05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -379,6 +379,34 @@ expressed genes in DNA microarray experiments.") "This package implements some simple graph handling capabilities for R.") (license license:artistic2.0))) +(define-public r-codedepends + (package + (name "r-codedepends") + (version "0.6.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "CodeDepends" version)) + (sha256 + (base32 + "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) + (properties `((upstream-name . "CodeDepends"))) + (build-system r-build-system) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-graph" ,r-graph) + ("r-xml" ,r-xml))) + (home-page "http://cran.r-project.org/web/packages/CodeDepends") + (synopsis "Analysis of R code for reproducible research and code comprehension") + (description + "This package provides tools for analyzing R expressions or blocks of +code and determining the dependencies between them. It focuses on R scripts, +but can be used on the bodies of functions. There are many facilities +including the ability to summarize or get a high-level view of code, +determining dependencies between variables, code improvement suggestions.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-chippeakanno (package (name "r-chippeakanno") -- cgit v1.2.3 From 35c076e619c0a7c25456fceb2e694f76e0315db5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 9 Sep 2018 15:35:54 +0200 Subject: gnu: r-chippeakanno: Update to 3.14.2. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a47a5aad05..108f3c398f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -410,14 +410,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.14.1") + (version "3.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1cn1hfc3nvsf2n3563lkmvwjxfbiygx7f84zk683p89gy7zi1gyj")))) + "13rksc65lxxzyw11galh6xzvgzp5ii0gwiwpvrm395v2r17rhwsc")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f6e9976393c80d12b5f3235bf7fe593077cbc9d1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 8 Oct 2018 14:18:48 +0200 Subject: gnu: Add r-dnabarcodes. * gnu/packages/bioconductor.scm (r-dnabarcodes): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 108f3c398f..1b779855b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -886,3 +886,30 @@ Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and assess via modeling the rates that determines changes in mature mRNA levels.") (license license:gpl2))) + +(define-public r-dnabarcodes + (package + (name "r-dnabarcodes") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DNABarcodes" version)) + (sha256 + (base32 + "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x")))) + (properties `((upstream-name . "DNABarcodes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) + (home-page "https://bioconductor.org/packages/DNABarcodes") + (synopsis "Create and analyze DNA barcodes") + (description + "This package offers tools to create DNA barcode sets capable of +correcting insertion, deletion, and substitution errors. Existing barcodes +can be analyzed regarding their minimal, maximal and average distances between +barcodes. Finally, reads that start with a (possibly mutated) barcode can be +demultiplexed, i.e. assigned to their original reference barcode.") + (license license:gpl2))) -- cgit v1.2.3 From 09aa3d063a0eacf3fca8d4803fbb62bd7b1ee663 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 22 Oct 2018 13:00:06 +0200 Subject: gnu: Add r-ruvseq. * gnu/packages/bioconductor.scm (r-ruvseq): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b779855b2..92b67453f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -913,3 +913,29 @@ can be analyzed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e. assigned to their original reference barcode.") (license license:gpl2))) + +(define-public r-ruvseq + (package + (name "r-ruvseq") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RUVSeq" version)) + (sha256 + (base32 + "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj")))) + (properties `((upstream-name . "RUVSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-edaseq" ,r-edaseq) + ("r-edger" ,r-edger) + ("r-mass" ,r-mass))) + (home-page "https://github.com/drisso/RUVSeq") + (synopsis "Remove unwanted variation from RNA-Seq data") + (description + "This package implements methods to @dfn{remove unwanted variation} (RUV) +of Risso et al. (2014) for the normalization of RNA-Seq read counts between +samples.") + (license license:artistic2.0))) -- cgit v1.2.3 From 696e1ce263a7ed960ef6d2150d1f484b8bf7d3cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 30 Oct 2018 07:44:05 +0100 Subject: gnu: r-graph: Update to 1.58.2. * gnu/packages/bioconductor.scm (r-graph): Update to 1.58.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92b67453f6..6ce5c0dc96 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -363,13 +363,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.58.0") + (version "1.58.2") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759")))) + "07smbb3c30pr5r425g181xsg0rs5jx6x2q6xpwb5dqgicxrz30ga")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) -- cgit v1.2.3 From 6168692159812724b1a0233167fd1a02b44aba19 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:43:05 +0100 Subject: gnu: r-hpar: Update to 1.24.0. * gnu/packages/bioconductor.scm (r-hpar): Update to 1.24.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6ce5c0dc96..797d7d4f91 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -201,14 +201,14 @@ genomes and gene ID formats, largely based on the UCSC table browser.") (define-public r-hpar (package (name "r-hpar") - (version "1.22.2") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388")))) + "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") -- cgit v1.2.3 From 98652568a42fcdb09c05e137fba96196b00d6c4e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:43:32 +0100 Subject: gnu: r-diffbind: Update to 2.10.0. * gnu/packages/bioconductor.scm (r-diffbind): Update to 2.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 797d7d4f91..72e43ae82d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -247,14 +247,14 @@ region sets and other genomic features.") (define-public r-diffbind (package (name "r-diffbind") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish")))) + "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From f1c606ce8c4214f41944f93da4c8a4a30ec71e8a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:43:55 +0100 Subject: gnu: r-marray: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-marray): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 72e43ae82d..adc4749ba2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -465,12 +465,12 @@ enrichedGO (addGeneIDs).") (define-public r-marray (package (name "r-marray") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d")))) + (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) -- cgit v1.2.3 From 46cdceef4c13f8d5f57f093e1aded95a1e04a265 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:44:12 +0100 Subject: gnu: r-cghbase: Update to 1.42.0. * gnu/packages/bioconductor.scm (r-cghbase): Update to 1.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index adc4749ba2..22140ef587 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -484,12 +484,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq")))) + (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9add0933d0a4dc5c142ce28fa424a0525e25390f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:44:29 +0100 Subject: gnu: r-cghcall: Update to 2.44.0. * gnu/packages/bioconductor.scm (r-cghcall): Update to 2.44.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22140ef587..7293d17719 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -504,12 +504,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz")))) + (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a92f523026a4b774b8da3b3d4dff2fb65f002a43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:44:50 +0100 Subject: gnu: r-qdnaseq: Update to 1.18.0. * gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.18.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7293d17719..165832a57b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -527,12 +527,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd")))) + (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 95ee4a466bbeb06d5815f9950f5b0a5ce830d7b5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:45:35 +0100 Subject: gnu: r-multtest: Update to 2.38.0. * gnu/packages/bioconductor.scm (r-multtest): Update to 2.38.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 165832a57b..d4ff89d8a7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -325,14 +325,14 @@ processing to visualization and annotation.") (define-public r-multtest (package (name "r-multtest") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0")))) + "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) -- cgit v1.2.3 From 14520b640eec571241d9f5b4dbd2fe237027b55d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:45:51 +0100 Subject: gnu: r-graph: Update to 1.60.0. * gnu/packages/bioconductor.scm (r-graph): Update to 1.60.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d4ff89d8a7..d4b336dfab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -363,13 +363,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.58.2") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "07smbb3c30pr5r425g181xsg0rs5jx6x2q6xpwb5dqgicxrz30ga")))) + "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) -- cgit v1.2.3 From 57d2fcd9eeb0c7b04db0fa890c1d23e9c796a868 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:46:21 +0100 Subject: gnu: r-chippeakanno: Update to 3.16.0. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.16.0. [propagated-inputs]: Remove r-biocinstaller; add r-biocmanager. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d4b336dfab..368691d1cc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -410,18 +410,19 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.14.2") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "13rksc65lxxzyw11galh6xzvgzp5ii0gwiwpvrm395v2r17rhwsc")))) + "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) ("r-biostrings" ,r-biostrings) ("r-delayedarray" ,r-delayedarray) ("r-go-db" ,r-go-db) @@ -437,7 +438,6 @@ determining dependencies between variables, code improvement suggestions.") ("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) -- cgit v1.2.3 From 4728e2751168eda6b2e211c9c74be21c22fe6f6b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:46:58 +0100 Subject: gnu: r-bayseq: Update to 2.16.0. * gnu/packages/bioconductor.scm (r-bayseq): Update to 2.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 368691d1cc..82733645b8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -559,14 +559,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg")))) + "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From aa802eafb66fc861f70292eb6674540aeac8db1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:47:22 +0100 Subject: gnu: r-chipcomp: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 82733645b8..8de8d5b233 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -585,14 +585,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs")))) + "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e9427b2c7852cbc02b06e91b1d5503f5f02211d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:47:38 +0100 Subject: gnu: r-ripseeker: Update to 1.22.0. * gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.22.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8de8d5b233..7c95847400 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -292,14 +292,14 @@ occupancy (overlap) analysis and plotting functions.") (define-public r-ripseeker (package (name "r-ripseeker") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 - "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi")))) + "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e22e462b3394a230400387b9c47b51a4f6bbb997 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:48:03 +0100 Subject: gnu: r-riboprofiling: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c95847400..ae72e43686 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -619,14 +619,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0")))) + "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c4fed658a934b97d1feaed4970e51f496cc39b23 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:48:22 +0100 Subject: gnu: r-riboseqr: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae72e43686..e079e63636 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -658,14 +658,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn")))) + "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From bbc4787cf26e3ecf695915fb7ed1e47ecee31ba6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:48:38 +0100 Subject: gnu: r-interactionset: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-interactionset): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e079e63636..f522735252 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -686,14 +686,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n")))) + "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) -- cgit v1.2.3 From 5f2d0e635e07039774422a1103e773a401dd87d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:48:55 +0100 Subject: gnu: r-genomicinteractions: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f522735252..ee37d98974 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -718,14 +718,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q")))) + "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) -- cgit v1.2.3 From b858338c7690bf7119feda9e59fb44d7888065c3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:49:13 +0100 Subject: gnu: r-ctc: Update to 1.56.0. * gnu/packages/bioconductor.scm (r-ctc): Update to 1.56.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee37d98974..dec94a09f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -757,14 +757,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9")))) + "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") -- cgit v1.2.3 From 6ea9ae9c3945d0ec6245ace9d0330f7821b64ed8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:49:28 +0100 Subject: gnu: r-goseq: Update to 1.34.0. * gnu/packages/bioconductor.scm (r-goseq): Update to 1.34.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dec94a09f4..0f88b37ccf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -777,14 +777,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l")))) + "1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 016afac30f0279a5b19e88765c1cefbbd47f62dc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:49:45 +0100 Subject: gnu: r-glimma: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-glimma): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f88b37ccf..4a61854a9b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -803,14 +803,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "1.8.2") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s")))) + "0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c348cfed74793864126d14b95a0d036b02e44b49 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:49:59 +0100 Subject: gnu: r-rots: Update to 1.10.0. * gnu/packages/bioconductor.scm (r-rots): Update to 1.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a61854a9b..18b08b739b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -830,14 +830,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3")))) + "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6f1e1d0f884b6e79543d46abf5c94aee50838f4f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:50:14 +0100 Subject: gnu: r-inspect: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 18b08b739b..576ab185b5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -854,14 +854,14 @@ in omics data.") (define-public r-inspect (package (name "r-inspect") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p")))) + "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 318bcbc4511ee1fcb7c71f74493443e0bb57f0d1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:50:30 +0100 Subject: gnu: r-dnabarcodes: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.12.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 576ab185b5..5855b02630 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -890,14 +890,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x")))) + "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 286157dc49d9b32ccb918759719f9bbbd5ff99bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:50:52 +0100 Subject: gnu: Add r-biocneighbors. * gnu/packages/bioconductor.scm (r-biocneighbors): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5855b02630..065dbdb6d5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -939,3 +939,32 @@ demultiplexed, i.e. assigned to their original reference barcode.") of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.") (license license:artistic2.0))) + +(define-public r-biocneighbors + (package + (name "r-biocneighbors") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocNeighbors" version)) + (sha256 + (base32 + "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll")))) + (properties `((upstream-name . "BiocNeighbors"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-rcpp" ,r-rcpp) + ("r-rcppannoy" ,r-rcppannoy) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/BiocNeighbors") + (synopsis "Nearest Neighbor Detection for Bioconductor packages") + (description + "This package implements exact and approximate methods for nearest +neighbor detection, in a framework that allows them to be easily switched +within Bioconductor packages or workflows. The exact algorithm is implemented +using pre-clustering with the k-means algorithm. Functions are also provided +to search for all neighbors within a given distance. Parallelization is +achieved for all methods using the BiocParallel framework.") + (license license:gpl3))) -- cgit v1.2.3 From ed35d7ca1fad410cf8ffaf664ca0800f403fb902 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:51:06 +0100 Subject: gnu: r-ruvseq: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.16.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 065dbdb6d5..ef5c799917 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -917,14 +917,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj")))) + "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d639d8884c85584e2487ed08fd8b1faca826e982 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 7 Nov 2018 11:51:30 +0100 Subject: gnu: r-regioner: Update to 1.14.0. * gnu/packages/bioconductor.scm (r-regioner): Update to 1.14.0. [propagated-inputs]: Add r-biostrings. --- gnu/packages/bioconductor.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ef5c799917..bab6b2b64d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -219,23 +219,24 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb")))) + "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs - `(("r-memoise" ,r-memoise) - ("r-genomicranges" ,r-genomicranges) + `(("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) - ("r-rtracklayer" ,r-rtracklayer) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-memoise" ,r-memoise) + ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") -- cgit v1.2.3 From 8a587c89af55d7fa858a65fe717cfbfbe84b0e1e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Nov 2018 16:45:21 +0100 Subject: gnu: Add r-savr. * gnu/packages/bioconductor.scm (r-savr): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bab6b2b64d..bc13460299 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -969,3 +969,29 @@ using pre-clustering with the k-means algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.") (license license:gpl3))) + +(define-public r-savr + (package + (name "r-savr") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "savR" version)) + (sha256 + (base32 + "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7")))) + (properties `((upstream-name . "savR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-xml" ,r-xml))) + (home-page "https://github.com/bcalder/savR") + (synopsis "Parse and analyze Illumina SAV files") + (description + "This package provides tools to parse Illumina Sequence Analysis +Viewer (SAV) files, access data, and generate QC plots.") + (license license:agpl3+))) -- cgit v1.2.3 From a961ae469cf81797df34f22eef0f0f5ca1a21e07 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Nov 2018 17:09:14 +0100 Subject: gnu: Add r-destiny. * gnu/packages/bioconductor.scm (r-destiny): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bc13460299..95c722ac40 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -970,6 +970,41 @@ to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.") (license license:gpl3))) +(define-public r-destiny + (package + (name "r-destiny") + (version "2.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "destiny" version)) + (sha256 + (base32 + "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-fnn" ,r-fnn) + ("r-ggthemes" ,r-ggthemes) + ("r-hmisc" ,r-hmisc) + ("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-proxy" ,r-proxy) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-scales" ,r-scales) + ("r-scatterplot3d" ,r-scatterplot3d) + ("r-smoother" ,r-smoother) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-vim" ,r-vim))) + (home-page "https://bioconductor.org/packages/destiny/") + (synopsis "Create and plot diffusion maps") + (description "This package provides tools to create and plot diffusion +maps.") + ;; Any version of the GPL + (license license:gpl3+))) + (define-public r-savr (package (name "r-savr") -- cgit v1.2.3 From 41ffc214e4839aa50e9957388749772e91a3f533 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 27 Nov 2018 23:23:20 +0100 Subject: gnu: Add r-chipexoqual. * gnu/packages/bioconductor.scm (r-chipexoqual): New variable. --- gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 95c722ac40..e7f11dead3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1030,3 +1030,41 @@ maps.") "This package provides tools to parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.") (license license:agpl3+))) + +(define-public r-chipexoqual + (package + (name "r-chipexoqual") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPexoQual" version)) + (sha256 + (base32 + "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp")))) + (properties `((upstream-name . "ChIPexoQual"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-biovizbase" ,r-biovizbase) + ("r-broom" ,r-broom) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-hexbin" ,r-hexbin) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/keleslab/ChIPexoQual") + (synopsis "Quality control pipeline for ChIP-exo/nexus data") + (description + "This package provides a quality control pipeline for ChIP-exo/nexus +sequencing data.") + (license license:gpl2+))) -- cgit v1.2.3