diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 141 |
1 files changed, 141 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e54c9ccf2b..d532360f7e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2098,6 +2098,96 @@ impute GReX can be trained with a training dataset where the real total expression values are known.") (license license:gpl3))) +(define-public r-affyilm + (package + (name "r-affyilm") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyILM" version)) + (sha256 + (base32 "0i2hjaqjz06ym5kbw5da1h3cahc630mjwljsji1l2ks0gjcipll0")))) + (properties `((upstream-name . "affyILM"))) + (build-system r-build-system) + (propagated-inputs + (list r-affxparser + r-affy + r-biobase + r-gcrma)) + (home-page "https://bioconductor.org/packages/affyILM") + (synopsis + "Linear model of background subtraction and the Langmuir isotherm") + (description + "The affyILM package is a preprocessing tool which estimates gene +expression levels for Affymetrix Gene Chips. Input from physical chemistry is +employed to first background subtract intensities before calculating +concentrations on behal of the Langmuir model.") + (license license:gpl3))) + +(define-public r-affylmgui + (package + (name "r-affylmgui") + (version "1.72.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affylmGUI" version)) + (sha256 + (base32 "0jds73pxqf522wcg8qd4b4k1qbhn51av5md1nhgcdnb6is0lzvxi")))) + (properties `((upstream-name . "affylmGUI"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-affyio + r-affyplm + r-annotationdbi + r-biocgenerics + r-biocmanager + r-gcrma + r-limma + r-r2html + r-tkrplot + r-xtable)) + (home-page "https://bioinf.wehi.edu.au/affylmGUI/") + (synopsis "GUI for limma package with Affymetrix microarrays") + (description + "This package provides a @acronym{GUI, Graphical User Interface} for +analysis of Affymetrix microarray gene expression data using the affy and +limma packages.") + (license license:gpl2+))) + +(define-public r-affyplm + (package + (name "r-affyplm") + (version "1.74.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyPLM" version)) + (sha256 + (base32 "0f0faxjzlg0znhjfvf1490yc54npkx659jx76cddm5hk7q0blv3v")))) + (properties `((upstream-name . "affyPLM"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-affy + r-biobase + r-biocgenerics + r-gcrma + r-preprocesscore + r-zlibbioc)) + (home-page "https://github.com/bmbolstad/affyPLM") + (synopsis "Methods for fitting probe-level models") + (description + "The affyPLM provides a package that extends and improves the +functionality of the base affy package. For speeding up the runs, it includes +routines that make heavy use of compiled code. The central focus is on +implementation of methods for fitting probe-level models and tools using these +models. @acronym{PLM, probe-level models} based quality assessment tools are +also provided.") + (license license:gpl2+))) + (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") @@ -2617,6 +2707,57 @@ Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.") (license license:artistic2.0))) +(define-public r-annotationhubdata + (package + (name "r-annotationhubdata") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationHubData" version)) + (sha256 + (base32 "0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95")))) + (properties `((upstream-name . "AnnotationHubData"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'install 'set-home + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-annotationdbi + r-annotationforge + r-annotationhub + r-biobase + r-bioccheck + r-biocgenerics + r-biocmanager + r-biocviews + r-biostrings + r-dbi + r-futile-logger + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-jsonlite + r-organismdbi + r-rcurl + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AnnotationHubData") + (synopsis "Transform public data resources into Bioconductor data structures") + (description + "This package provides tools to acquire, annotate, convert and store data +for use in Bioconductor’s AnnotationHub.") + (license license:artistic2.0))) + (define-public r-anvil (package (name "r-anvil") |