signifinder

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see signifinder.

Implementations of transcriptional cancer signatures

Bioconductor version: 3.16

signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows computing signatures scores providing the only gene expression values and returns a single-sample score. Currently, signifinder contains 46 distinct signatures collected from the literature.

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BiomedicalInformatics, GeneExpression, GeneTarget, ImmunoOncology, Microarray, RNASeq, ReportWriting, Software, Visualization

Version 1.0.0

In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)

License AGPL-3

Depends R (>= 4.2.0)

Imports ggplot2, org.Hs.eg.db, patchwork, AnnotationDbi, BiocGenerics, ComplexHeatmap, 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

System Requirements

URL https://github.com/CaluraLab/signifinder

Bug Reports https://github.com/CaluraLab/signifinder/issues

Suggests BiocStyle, knitr, kableExtra, testthat (>= 3.0.0), edgeR, limma

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package signifinder_1.0.0.tar.gz

Windows Binary signifinder_1.0.0.zip (64-bit only)

macOS Binary (x86_64) signifinder_1.0.0.tgz

macOS Binary (arm64) signifinder_1.0.0.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 3.16 Source Archive