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1 | ;;; GNU Guix --- Functional package management for GNU |
2 | ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net> | |
183ce988 | 3 | ;;; Copyright © 2018 Roel Janssen <roel@gnu.org> |
fa596599 RW |
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) | |
183ce988 | 25 | #:use-module (gnu packages) |
a5b56a53 RJ |
26 | #:use-module (gnu packages cran) |
27 | #:use-module (gnu packages compression) | |
183ce988 RJ |
28 | #:use-module (gnu packages statistics) |
29 | #:use-module (gnu packages bioinformatics)) | |
fa596599 RW |
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))) | |
183ce988 RJ |
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))) | |
a5b56a53 RJ |
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))) | |
6d94bf6b RJ |
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))) | |
a6ae9ffd RJ |
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))) |