signifinder

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see signifinder.

Collection and implementation of public transcriptional cancer signatures

Bioconductor version: 3.21

signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures coming from public literature, based on gene expression values, and return single-sample (-cell/-spot) scores. Currently, signifinder collects more than 70 distinct signatures, relating to multiple tumors and multiple cancer processes.

Author: Stefania Pirrotta [cre, aut] ORCID iD ORCID: 0009-0004-0030-217X , Enrica Calura [aut] ORCID iD ORCID: 0000-0001-8463-2432

Maintainer: Stefania Pirrotta <stefania.pirrotta at phd.unipd.it>

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

Installation

To install this package, start R (version "4.5") 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, GeneSignaling, GeneTarget, ImmunoOncology, Microarray, RNASeq, ReportWriting, SingleCell, Software, Spatial, Visualization

Version 1.10.0

In Bioconductor since BioC 3.16 (R-4.2) (3 years)

License AGPL-3

Depends R (>= 4.4.0)

System Requirements

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

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

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

Linking To

Enhances

Depends On Me

Imports Me

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Links To Me

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Package Archives

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

Source Package signifinder_1.10.0.tar.gz

Windows Binary (x86_64) signifinder_1.10.0.zip

macOS Binary (x86_64) signifinder_1.10.0.tgz

macOS Binary (arm64) signifinder_1.10.0.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/

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