signifinder

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

Collection and implementation of public transcriptional cancer signatures


Bioconductor version: Development (3.21)

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 more than 60 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.

Author: Stefania Pirrotta [cre, aut] (ORCID: ), Enrica Calura [aut] (ORCID: )

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")

# 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

Reference Manual PDF

Details

biocViews BiomedicalInformatics, GeneExpression, GeneSignaling, GeneTarget, ImmunoOncology, Microarray, RNASeq, ReportWriting, SingleCell, Software, Spatial, Visualization
Version 1.9.0
In Bioconductor since BioC 3.16 (R-4.2) (2 years)
License AGPL-3
Depends R (>= 4.3.0)
Imports AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV, cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges, GSVA, IRanges, magrittr, matrixStats, maxstat, methods, openair, org.Hs.eg.db, patchwork, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, sparrow, SpatialExperiment, stats, SummarizedExperiment, survival, survminer, viridis
System Requirements
URL https://github.com/CaluraLab/signifinder
Bug Reports https://github.com/CaluraLab/signifinder/issues
See More
Suggests BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat (>= 3.0.0)
Linking To
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Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/signifinder/
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