gnu: Add r-assessorf.

[jackhill/guix/guix.git] / gnu / packages / bioconductor.scm

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ad20602..67a62fa 100644 (file)
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2317,6 +2317,136 @@ reproducible gene expression signatures capable of accurately distinguishing
 tumor samples from healthy controls.")
     (license license:artistic2.0)))
 
+(define-public r-assessorf
+  (package
+    (name "r-assessorf")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AssessORF" version))
+              (sha256
+               (base32
+                "1l87bpny9k3jbzbzmb9h2ijvblrj471gqv26fyzbvb3vr6y406z7"))))
+    (properties `((upstream-name . "AssessORF")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-decipher
+           r-genomicranges
+           r-iranges))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AssessORF")
+    (synopsis "Assess gene predictions using proteomics and evolutionary conservation")
+    (description
+     "In order to assess the quality of a set of predicted genes for a genome,
+evidence must first be mapped to that genome.  Next, each gene must be
+categorized based on how strong the evidence is for or against that gene.  The
+AssessORF package provides the functions and class structures necessary for
+accomplishing those tasks, using proteomics hits and evolutionarily conserved
+start codons as the forms of evidence.")
+    (license license:gpl3)))
+
+(define-public r-asset
+  (package
+    (name "r-asset")
+    (version "2.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ASSET" version))
+              (sha256
+               (base32
+                "029acl5k9d4hnvy3jia9cr4rk6w31zn8b5s79i6lazq1cp236hbg"))))
+    (properties `((upstream-name . "ASSET")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-mass r-msm r-rmeta))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ASSET")
+    (synopsis
+     "Subset-based association analysis of heterogeneous traits and subtypes")
+    (description
+     "This package is an R program for the subset-based analysis of
+heterogeneous traits and disease subtypes.  ASSET allows the user to search
+through all possible subsets of z-scores to identify the subset of traits
+giving the best meta-analyzed z-score.  Further, it returns a p-value
+adjusting for the multiple-testing involved in the search.  It also allows for
+searching for the best combination of disease subtypes associated with each
+variant.")
+    (license license:gpl2)))
+
+(define-public r-atena
+  (package
+    (name "r-atena")
+    (version "1.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "atena" version))
+              (sha256
+               (base32
+                "0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp"))))
+    (properties `((upstream-name . "atena")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-annotationhub
+           r-biocgenerics
+           r-biocparallel
+           r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-iranges
+           r-matrix
+           r-rsamtools
+           r-s4vectors
+           r-scales
+           r-sparsematrixstats
+           r-squarem
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/functionalgenomics/atena")
+    (synopsis "Analysis of transposable elements")
+    (description
+     "The atena package quantifies expression of @dfn{TEs} (transposable
+elements) from RNA-seq data through different methods, including ERVmap,
+TEtranscripts and Telescope.  A common interface is provided to use each of
+these methods, which consists of building a parameter object, calling the
+quantification function with this object and getting a
+@code{SummarizedExperiment} object as an output container of the quantified
+expression profiles.  The implementation allows quantifing TEs and gene
+transcripts in an integrated manner.")
+    (license license:artistic2.0)))
+
+(define-public r-atsnp
+  (package
+    (name "r-atsnp")
+    (version "1.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "atSNP" version))
+              (sha256
+               (base32
+                "0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz"))))
+    (properties `((upstream-name . "atSNP")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocfilecache
+           r-biocparallel
+           r-bsgenome
+           r-data-table
+           r-ggplot2
+           r-lifecycle
+           r-motifstack
+           r-rappdirs
+           r-rcpp
+           r-testthat))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/sunyoungshin/atSNP")
+    (synopsis
+     "Affinity test for identifying regulatory single nucleotide polymorphisms")
+    (description
+     "The atSNP package performs affinity tests of motif matches with the
+@dfn{SNP} (single nucleotide polymorphism) or the reference genomes and
+SNP-led changes in motif matches.")
+    (license license:gpl2)))
+
 (define-public r-attract
   (package
     (name "r-attract")