diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 79 |
1 files changed, 79 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74620a2cbe..ea43bf2fdf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5089,6 +5089,41 @@ by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.") (license license:expat))) +(define-public r-rcistarget + (package + (name "r-rcistarget") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RcisTarget" version)) + (sha256 + (base32 + "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd")))) + (properties `((upstream-name . "RcisTarget"))) + (build-system r-build-system) + (propagated-inputs + `(("r-aucell" ,r-aucell) + ("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) + ("r-feather" ,r-feather) + ("r-gseabase" ,r-gseabase) + ("r-r-utils" ,r-r-utils) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://aertslab.org/#scenic") + (synopsis "Identify transcription factor binding motifs enriched on a gene list") + (description + "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) +over-represented on a gene list. In a first step, RcisTarget selects DNA +motifs that are significantly over-represented in the surroundings of the +@dfn{transcription start site} (TSS) of the genes in the gene-set. This is +achieved by using a database that contains genome-wide cross-species rankings +for each motif. The motifs that are then annotated to TFs and those that have +a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for +each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. +genes in the gene-set that are ranked above the leading edge).") + (license license:gpl3))) + (define-public r-cicero (package (name "r-cicero") @@ -5151,3 +5186,47 @@ accessibility data.") `(("r-monocle3" ,r-monocle3) ,@(alist-delete "r-monocle" (package-propagated-inputs r-cicero))))))) + +(define-public r-cistopic + (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") + (revision "0")) + (package + (name "r-cistopic") + (version (git-version "0.2.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/cisTopic.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-aucell" ,r-aucell) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-dosnow" ,r-dosnow) + ("r-dt" ,r-dt) + ("r-feather" ,r-feather) + ("r-fitdistrplus" ,r-fitdistrplus) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-lda" ,r-lda) + ("r-matrix" ,r-matrix) + ("r-plyr" ,r-plyr) + ("r-rcistarget" ,r-rcistarget) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/aertslab/cisTopic") + (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") + (description + "The sparse nature of single cell epigenomics data can be overruled using +probabilistic modelling methods such as @dfn{Latent Dirichlet +Allocation} (LDA). This package allows the probabilistic modelling of +cis-regulatory topics (cisTopics) from single cell epigenomics data, and +includes functionalities to identify cell states based on the contribution of +cisTopics and explore the nature and regulatory proteins driving them.") + (license license:gpl3)))) |