signifinder
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
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 | 1.9.1 |
| 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 |