TMSig

Tools for Molecular Signatures


Bioconductor version: Release (3.20)

The TMSig package contains tools to prepare, analyze, and visualize named lists of sets, with an emphasis on molecular signatures (such as gene or kinase sets). It includes fast, memory efficient functions to construct sparse incidence and similarity matrices and filter, cluster, invert, and decompose sets. Additionally, bubble heatmaps can be created to visualize the results of any differential or molecular signatures analysis.

Author: Tyler Sagendorf [aut, cre] , Di Wu [ctb], Gordon Smyth [ctb]

Maintainer: Tyler Sagendorf <tyler.sagendorf at pnnl.gov>

Citation (from within R, enter citation("TMSig")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TMSig")

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("TMSig")
An Introduction to TMSig HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, GeneSetEnrichment, GraphAndNetwork, Pathways, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.20 (R-4.4) (< 6 months)
License GPL (>= 3)
Depends R (>= 4.4.0), limma
Imports circlize, ComplexHeatmap, data.table, grDevices, grid, GSEABase, Matrix, methods, stats, utils
System Requirements
URL https://github.com/EMSL-Computing/TMSig
Bug Reports https://github.com/EMSL-Computing/TMSig/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package TMSig_1.0.0.tar.gz
Windows Binary (x86_64) TMSig_1.0.0.zip (64-bit only)
macOS Binary (x86_64) TMSig_1.0.0.tgz
macOS Binary (arm64) TMSig_0.99.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/TMSig
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TMSig
Bioc Package Browser https://code.bioconductor.org/browse/TMSig/
Package Short Url https://bioconductor.org/packages/TMSig/
Package Downloads Report Download Stats