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signifinder
This is thereleased version of signifinder; for the devel version, seesignifinder.
Collection and implementation of public transcriptional cancer signatures
Bioconductor version: Release (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("signifinder")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("signifinder")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("signifinder")| signifinder vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics,GeneExpression,GeneSignaling,GeneTarget,ImmunoOncology,Microarray,RNASeq,ReportWriting,SingleCell,Software,Spatial,Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 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
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | signifinder_1.12.0.tar.gz |
| Windows Binary (x86_64) | signifinder_1.12.0.zip |
| macOS Binary (x86_64) | signifinder_1.12.0.tgz |
| macOS Binary (arm64) | signifinder_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/signifinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/signifinder |
| Bioc Package Browser | https://code.bioconductor.org/browse/signifinder/ |
| Package Short Url | https://bioconductor.org/packages/signifinder/ |
| Package Downloads Report | Download Stats |