TMSig

This is the development version of TMSig; for the stable release version, see TMSig.

Tools for Molecular Signatures

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DOI: 10.18129/B9.bioc.TMSig

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0000-0003-1552-4870 , 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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, GeneSetEnrichment, GraphAndNetwork, Pathways, Software, Visualization

Version 1.5.0

In Bioconductor since BioC 3.20 (R-4.4) (1 year)

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

Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)

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Build Report Build Report

Package Archives

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

Source Package TMSig_1.5.0.tar.gz

Windows Binary (x86_64) TMSig_1.5.0.zip

macOS Binary (x86_64) TMSig_1.5.0.tgz

macOS Binary (arm64) TMSig_1.5.0.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/

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