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:
Maintainer: Stefania Pirrotta <stefania.pirrotta at phd.unipd.it>
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 |
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 | |
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 | |
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/ |
Package Downloads Report | Download Stats |