diff options
| author | pjotrp | 2016-01-22 11:57:01 +0300 |
|---|---|---|
| committer | pjotrp | 2016-01-22 11:57:01 +0300 |
| commit | bd27d282ef25ae04daa3ef7ef8413b5fedce527d (patch) | |
| tree | 01ed61883e529cc244763b509f270fbb6ee99d3c /gn | |
| parent | b88ec82e4de27f370a10bc41b9403780b7b30768 (diff) | |
| download | guix-bioinformatics-bd27d282ef25ae04daa3ef7ef8413b5fedce527d.tar.gz | |
add qtlreaper
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 35 |
1 files changed, 35 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 787c2a9..43befb4 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -120,6 +120,41 @@ "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.") (license license:gpl2+))) +(define-public qtlreaper + (package + (name "qtlreaper") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/qtlreaper/qtlreaper-" version ".tar.gz" + ;; "http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb")) + )) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0rbf030940nbbbkggdq2dxiy3c0jv8l4y3vvyfxhqimgj0qv3l1x")))) + (build-system python-build-system) + ;; (native-inputs + ;; `(("python-setuptools" ,python-setuptools))) + (arguments + `(#:python ,python-2 + #:tests? #f)) ; no 'setup.py test' + (home-page "http://qtlreaper.sourceforge.net/") + (synopsis "Tool for scanning expression data for QTLs") + (description + "It is essentially the batch-oriented version of WebQTL. It +requires, as input, expression data from members of a set of +recombinant inbred lines and genotype information for the same +lines. It searches for an association between each expression trait +and all genotypes and evaluates that association by a permutation +test. For the permutation test, it performs only as many permutations +as are necessary to define the empirical P-value to a reasonable +precision. It also performs bootstrap resampling to estimate the +confidence region for the location of a putative QTL.") + (license license:gpl2))) + (define-public genenetwork2 (let ((commit "9e9475053")) |