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 phd.unipd.it>

Citation (from within R, enter citation("signifinder")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("signifinder")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("signifinder")

signifinder vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

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, org.Hs.eg.db, 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
Linking To
Suggests	BiocStyle, knitr, kableExtra, testthat (>= 3.0.0), edgeR, limma
System Requirements
Enhances
URL	https://github.com/CaluraLab/signifinder
Bug Reports	https://github.com/CaluraLab/signifinder/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	signifinder_1.2.1.tar.gz
Windows Binary	signifinder_1.2.1.zip
macOS Binary (x86_64)	signifinder_1.2.1.tgz
macOS Binary (arm64)	signifinder_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/signifinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/signifinder
Bioc Package Browser	https://code.bioconductor.org/browse/signifinder/
Package Short Url	https://bioconductor.org/packages/signifinder/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive