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Bioconductor - signifinder (development version)

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 (3.22)

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")): 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("signifinder")
Details biocViews BiomedicalInformatics, GeneExpression, GeneSignaling, GeneTarget, ImmunoOncology, Microarray, RNASeq, ReportWriting, SingleCell, Software, Spatial, Visualization Version 1.11.0 In Bioconductor since BioC 3.16 (R-4.2) (2.5 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 See More Package Archives

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

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