signifinder
This is the released version of signifinder; for the devel version, see signifinder.
Collection and implementation of public transcriptional cancer signatures
Bioconductor version: Release (3.23)
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]
, Enrica Calura [aut]
Maintainer: Stefania Pirrotta <stefania.pirrotta at phd.unipd.it>
citation("signifinder")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")| signifinder vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, GeneExpression, GeneSignaling, GeneTarget, ImmunoOncology, Microarray, RNASeq, ReportWriting, SingleCell, Software, Spatial, Visualization |
| Version | 1.13.0 |
| 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 |
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 | signifinder_1.13.0.tar.gz |
| Windows Binary (x86_64) | signifinder_1.13.0.zip |
| macOS Binary (big-sur-x86_64) | signifinder_1.13.0.tgz |
| macOS Binary (sonoma-arm64) | signifinder_1.13.0.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 |