signifinder

DOI: 10.18129/B9.bioc.signifinder  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see signifinder.

Implementations of transcriptional cancer signatures

Bioconductor version: 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>

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")

 

HTML	R Script	signifinder vignette
PDF		Reference Manual
Text		NEWS

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
LinkingTo
Suggests	BiocStyle, knitr, kableExtra, testthat (>= 3.0.0), edgeR, limma
SystemRequirements
Enhances
URL	https://github.com/CaluraLab/signifinder
BugReports	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