diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7906a29b00..90ca2ae52a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -55,6 +55,7 @@ #:use-module (gnu packages java) #:use-module (gnu packages javascript) #:use-module (gnu packages maths) + #:use-module (gnu packages ncurses) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) #:use-module (gnu packages perl) @@ -10849,6 +10850,49 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-sictools + (package + (name "r-sictools") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SICtools" version)) + (sha256 + (base32 "0bcajjvkaxmr8bdij8xln7a3nmxbm7jkjvg2v6p8kd0xr3q9a70q")))) + (properties `((upstream-name . "SICtools"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-curses + (lambda _ + (substitute* "src/Makefile" + (("^LIBCURSES.*") + "LIBCURSES=-lncurses\n"))))))) + (propagated-inputs (list r-biostrings + r-doparallel + r-genomicranges + r-iranges + r-matrixstats + r-plyr + r-rsamtools + r-stringr)) + (inputs (list ncurses)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/SICtools") + (synopsis + "Find SNV/Indel differences between two bam files with near relationship") + (description + "This package is to find SNV/Indel differences between two @file{bam} +files with near relationship in a way of pairwise comparison through each base +position across the genome region of interest. The difference is inferred by +Fisher test and euclidean distance, the input of which is the base +count (A,T,G,C) in a given position and read counts for indels that span no +less than 2bp on both sides of indel region.") + (license license:gpl2+))) + (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") |