signifinder

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

Collection and implementation of public transcriptional cancer signatures

Bioconductor version: Development (3.24)

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: 0009-0004-0030-217X , Enrica Calura [aut] ORCID: 0000-0001-8463-2432

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

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

Stefania Pirrotta, Enrica Calura. signifinder: Collection and implementation of public transcriptional cancer signatures. doi:10.18129/B9.bioc.signifinder, R package version 1.15.0, https://bioconductor.org/packages/signifinder.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("signifinder")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, GeneExpression, GeneSignaling, GeneTarget, ImmunoOncology, Microarray, RNASeq, ReportWriting, SingleCell, Software, Spatial, Visualization
Version	1.15.0
In Bioconductor since	BioC 3.16 (R-4.2) (4 years)
License	AGPL-3
Depends	R (>= 4.4.0)
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, SpatialExperiment, stats, scales, SummarizedExperiment, survival, survminer, viridis
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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Build Report	Build Report, r-universe

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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/
Package Downloads Report	Download Stats