| 1 | ;;; GNU Guix --- Functional package management for GNU |
| 2 | ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> |
| 3 | ;;; Copyright © 2018 Roel Janssen <roel@gnu.org> |
| 4 | ;;; |
| 5 | ;;; This file is part of GNU Guix. |
| 6 | ;;; |
| 7 | ;;; GNU Guix is free software; you can redistribute it and/or modify it |
| 8 | ;;; under the terms of the GNU General Public License as published by |
| 9 | ;;; the Free Software Foundation; either version 3 of the License, or (at |
| 10 | ;;; your option) any later version. |
| 11 | ;;; |
| 12 | ;;; GNU Guix is distributed in the hope that it will be useful, but |
| 13 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of |
| 14 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 15 | ;;; GNU General Public License for more details. |
| 16 | ;;; |
| 17 | ;;; You should have received a copy of the GNU General Public License |
| 18 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. |
| 19 | |
| 20 | (define-module (gnu packages bioconductor) |
| 21 | #:use-module ((guix licenses) #:prefix license:) |
| 22 | #:use-module (guix packages) |
| 23 | #:use-module (guix download) |
| 24 | #:use-module (guix build-system r) |
| 25 | #:use-module (gnu packages) |
| 26 | #:use-module (gnu packages cran) |
| 27 | #:use-module (gnu packages compression) |
| 28 | #:use-module (gnu packages statistics) |
| 29 | #:use-module (gnu packages bioinformatics)) |
| 30 | |
| 31 | (define-public r-hpar |
| 32 | (package |
| 33 | (name "r-hpar") |
| 34 | (version "1.20.0") |
| 35 | (source |
| 36 | (origin |
| 37 | (method url-fetch) |
| 38 | (uri (bioconductor-uri "hpar" version)) |
| 39 | (sha256 |
| 40 | (base32 |
| 41 | "0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8")))) |
| 42 | (build-system r-build-system) |
| 43 | (home-page "https://bioconductor.org/packages/hpar/") |
| 44 | (synopsis "Human Protein Atlas in R") |
| 45 | (description "This package provides a simple interface to and data from |
| 46 | the Human Protein Atlas project.") |
| 47 | (license license:artistic2.0))) |
| 48 | |
| 49 | (define-public r-regioner |
| 50 | (package |
| 51 | (name "r-regioner") |
| 52 | (version "1.10.0") |
| 53 | (source |
| 54 | (origin |
| 55 | (method url-fetch) |
| 56 | (uri (bioconductor-uri "regioneR" version)) |
| 57 | (sha256 |
| 58 | (base32 |
| 59 | "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp")))) |
| 60 | (properties `((upstream-name . "regioneR"))) |
| 61 | (build-system r-build-system) |
| 62 | (propagated-inputs |
| 63 | `(("r-memoise" ,r-memoise) |
| 64 | ("r-genomicranges" ,r-genomicranges) |
| 65 | ("r-bsgenome" ,r-bsgenome) |
| 66 | ("r-rtracklayer" ,r-rtracklayer) |
| 67 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 68 | ("r-iranges" ,r-iranges))) |
| 69 | (home-page "https://bioconductor.org/packages/regioneR/") |
| 70 | (synopsis "Association analysis of genomic regions") |
| 71 | (description "This package offers a statistical framework based on |
| 72 | customizable permutation tests to assess the association between genomic |
| 73 | region sets and other genomic features.") |
| 74 | (license license:artistic2.0))) |
| 75 | |
| 76 | (define-public r-diffbind |
| 77 | (package |
| 78 | (name "r-diffbind") |
| 79 | (version "2.6.6") |
| 80 | (source |
| 81 | (origin |
| 82 | (method url-fetch) |
| 83 | (uri (bioconductor-uri "DiffBind" version)) |
| 84 | (sha256 |
| 85 | (base32 |
| 86 | "1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp")))) |
| 87 | (properties `((upstream-name . "DiffBind"))) |
| 88 | (build-system r-build-system) |
| 89 | (inputs |
| 90 | `(("zlib" ,zlib))) |
| 91 | (propagated-inputs |
| 92 | `(("r-amap" ,r-amap) |
| 93 | ("r-biocparallel" ,r-biocparallel) |
| 94 | ("r-deseq2" ,r-deseq2) |
| 95 | ("r-dplyr" ,r-dplyr) |
| 96 | ("r-edger" ,r-edger) |
| 97 | ("r-genomicalignments" ,r-genomicalignments) |
| 98 | ("r-ggrepel" ,r-ggrepel) |
| 99 | ("r-gplots" ,r-gplots) |
| 100 | ("r-iranges" ,r-iranges) |
| 101 | ("r-lattice" ,r-lattice) |
| 102 | ("r-limma" ,r-limma) |
| 103 | ("r-locfit" ,r-locfit) |
| 104 | ("r-rcolorbrewer" , r-rcolorbrewer) |
| 105 | ("r-rcpp" ,r-rcpp) |
| 106 | ("r-rsamtools" ,r-rsamtools) |
| 107 | ("r-s4vectors" ,r-s4vectors) |
| 108 | ("r-systempiper" ,r-systempiper) |
| 109 | ("r-zlibbioc" ,r-zlibbioc))) |
| 110 | (home-page "http://bioconductor.org/packages/DiffBind") |
| 111 | (synopsis "Differential binding analysis of ChIP-Seq peak data") |
| 112 | (description |
| 113 | "This package computes differentially bound sites from multiple |
| 114 | ChIP-seq experiments using affinity (quantitative) data. Also enables |
| 115 | occupancy (overlap) analysis and plotting functions.") |
| 116 | (license license:artistic2.0))) |
| 117 | |
| 118 | (define-public r-ripseeker |
| 119 | (package |
| 120 | (name "r-ripseeker") |
| 121 | (version "1.18.0") |
| 122 | (source |
| 123 | (origin |
| 124 | (method url-fetch) |
| 125 | (uri (bioconductor-uri "RIPSeeker" version)) |
| 126 | (sha256 |
| 127 | (base32 |
| 128 | "0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y")))) |
| 129 | (properties `((upstream-name . "RIPSeeker"))) |
| 130 | (build-system r-build-system) |
| 131 | (propagated-inputs |
| 132 | `(("r-s4vectors" ,r-s4vectors) |
| 133 | ("r-iranges" ,r-iranges) |
| 134 | ("r-genomicranges" ,r-genomicranges) |
| 135 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 136 | ("r-rsamtools" ,r-rsamtools) |
| 137 | ("r-genomicalignments" ,r-genomicalignments) |
| 138 | ("r-rtracklayer" ,r-rtracklayer))) |
| 139 | (home-page "http://bioconductor.org/packages/RIPSeeker") |
| 140 | (synopsis |
| 141 | "Identifying protein-associated transcripts from RIP-seq experiments") |
| 142 | (description |
| 143 | "This package infers and discriminates RIP peaks from RIP-seq alignments |
| 144 | using two-state HMM with negative binomial emission probability. While |
| 145 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides |
| 146 | a suite of bioinformatics tools integrated within this self-contained software |
| 147 | package comprehensively addressing issues ranging from post-alignments |
| 148 | processing to visualization and annotation.") |
| 149 | (license license:gpl2))) |
| 150 | |
| 151 | (define-public r-multtest |
| 152 | (package |
| 153 | (name "r-multtest") |
| 154 | (version "2.34.0") |
| 155 | (source |
| 156 | (origin |
| 157 | (method url-fetch) |
| 158 | (uri (bioconductor-uri "multtest" version)) |
| 159 | (sha256 |
| 160 | (base32 |
| 161 | "0n11rd49xl2vn3ldmfips7d3yb70l8npjcqsxyswr9ypjhgzkv9j")))) |
| 162 | (build-system r-build-system) |
| 163 | (propagated-inputs |
| 164 | `(("r-survival" ,r-survival) |
| 165 | ("r-biocgenerics" ,r-biocgenerics) |
| 166 | ("r-biobase" ,r-biobase) |
| 167 | ("r-mass" ,r-mass))) |
| 168 | (home-page "http://bioconductor.org/packages/multtest") |
| 169 | (synopsis "Resampling-based multiple hypothesis testing") |
| 170 | (description |
| 171 | "This package can do non-parametric bootstrap and permutation |
| 172 | resampling-based multiple testing procedures (including empirical Bayes |
| 173 | methods) for controlling the family-wise error rate (FWER), generalized |
| 174 | family-wise error rate (gFWER), tail probability of the proportion of |
| 175 | false positives (TPPFP), and false discovery rate (FDR). Several choices |
| 176 | of bootstrap-based null distribution are implemented (centered, centered |
| 177 | and scaled, quantile-transformed). Single-step and step-wise methods are |
| 178 | available. Tests based on a variety of T- and F-statistics (including |
| 179 | T-statistics based on regression parameters from linear and survival models |
| 180 | as well as those based on correlation parameters) are included. When probing |
| 181 | hypotheses with T-statistics, users may also select a potentially faster null |
| 182 | distribution which is multivariate normal with mean zero and variance |
| 183 | covariance matrix derived from the vector influence function. Results are |
| 184 | reported in terms of adjusted P-values, confidence regions and test statistic |
| 185 | cutoffs. The procedures are directly applicable to identifying differentially |
| 186 | expressed genes in DNA microarray experiments.") |
| 187 | (license license:lgpl3))) |