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signifinder

This is the development version of signifinder; for the stable release version, see signifinder.

Implementations of transcriptional cancer signatures

Bioconductor version: Development (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.1
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
See More
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_1.3.1.tar.gz
Windows Binary signifinder_1.3.1.zip
macOS Binary (x86_64) signifinder_1.3.1.tgz
macOS Binary (arm64)
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