DOI: 10.18129/B9.bioc.signifinder  

Implementations of transcriptional cancer signatures

Bioconductor version: Release (3.17)

signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains 46 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.

Author: Stefania Pirrotta [cre, aut] , Enrica Calura [aut]

Maintainer: Stefania Pirrotta <stefania.pirrotta at>

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biocViews BiomedicalInformatics, GeneExpression, GeneTarget, ImmunoOncology, Microarray, RNASeq, ReportWriting, SingleCell, Software, Spatial, Visualization
Version 1.2.1
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License AGPL-3
Depends R (>= 4.2.0)
Imports ggplot2,, patchwork, AnnotationDbi, BiocGenerics, ComplexHeatmap, cowplot, DGEobj.utils, GSVA, IRanges, SummarizedExperiment, consensusOV, dplyr, ensembldb, ggridges, grid, magrittr, matrixStats, maxstat, methods, openair, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, stats, survival, survminer, viridis
Suggests BiocStyle, knitr, kableExtra, testthat (>= 3.0.0), edgeR, limma
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