TMSig
This is the development version of TMSig; for the stable release version, see TMSig.
Tools for Molecular Signatures
Bioconductor version: Development (3.21)
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:
Maintainer: Tyler Sagendorf <tyler.sagendorf at pnnl.gov>
citation("TMSig")):
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("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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, GeneSetEnrichment, GraphAndNetwork, Pathways, Software, Visualization |
| Version | 1.1.0 |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TMSig_1.1.0.tar.gz |
| Windows Binary (x86_64) | TMSig_1.1.0.zip (64-bit only) |
| macOS Binary (x86_64) | TMSig_1.1.0.tgz |
| macOS Binary (arm64) | TMSig_1.1.0.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/ |
| Package Downloads Report | Download Stats |