TBSignatureProfiler

DOI: 10.18129/B9.bioc.TBSignatureProfiler    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler.

Profile RA-Seq Data Using TB Pathway Signatures

Bioconductor version: 3.11

Signatures of TB progression, TB disease, and other TB disease states have been created. This package makes it easy to profile RNA-Seq data using these signatures and common signature profiling tools including ASSIGN, GSVA, and ssGSEA.

Author: David Jenkins [aut, cre], Yue Zhao [aut], W. Evan Johnson [aut], Aubrey Odom [aut], Christian Love [aut]

Maintainer: David Jenkins <dfj at bu.edu>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("TBSignatureProfiler")

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("TBSignatureProfiler")

 

HTML	R Script	Introduction to the TBSignatureProfiler
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, Software
Version	1.0.0
In Bioconductor since	BioC 3.11 (R-4.0) (0.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0.0)
Imports	ASSIGN(>= 1.23.1), GSVA, SummarizedExperiment, S4Vectors, methods, BiocParallel, ComplexHeatmap, RColorBrewer, ggplot2, reshape2, circlize, glmnet, ROCit, bioDist, readr, boot, DESeq2, caret, ggfortify, e1071, DT, edgeR, singscore, gdata, shiny
LinkingTo
Suggests	testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/compbiomed/TBSignatureProfiler
BugReports	https://github.com/compbiomed/TBSignatureProfiler/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TBSignatureProfiler_1.0.0.tar.gz
Windows Binary	TBSignatureProfiler_1.0.0.zip
macOS 10.13 (High Sierra)	TBSignatureProfiler_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TBSignatureProfiler
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TBSignatureProfiler
Package Short Url	https://bioconductor.org/packages/TBSignatureProfiler/
Package Downloads Report	Download Stats