TBSignatureProfiler

DOI: 10.18129/B9.bioc.TBSignatureProfiler  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler.

Profile RNA-Seq Data Using TB Pathway Signatures

Bioconductor version: 3.16

Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates known signatures and provides computational tools to enlist their usage on other datasets. The TBSignatureProfiler makes it easy to profile RNA-Seq data using these signatures and includes common signature profiling tools including ASSIGN, GSVA, and ssGSEA. Original models for some gene signatures are also available. A shiny app provides some functionality alongside for detailed command line accessibility.

Author: Aubrey R. Odom-Mabey [aut, cre, dtm] , David Jenkins [aut, org] , Xutao Wang [aut], Yue Zhao [ctb] , Christian Love [ctb], W. Evan Johnson [aut]

Maintainer: Aubrey R. Odom-Mabey <aodom at bu.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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		LICENSE

Details

biocViews	DifferentialExpression, GeneExpression, Software
Version	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 years)
License	MIT + file LICENSE
Depends	R (>= 4.2.0)
Imports	ASSIGN(>= 1.23.1), BiocGenerics, BiocParallel, ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, GSVA, magrittr, methods, RColorBrewer, reshape2, rlang, ROCit, S4Vectors, singscore, stats, SummarizedExperiment
LinkingTo
Suggests	BiocStyle, caret, circlize, class, covr, dplyr, e1071, glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC, randomForest, rmarkdown, shiny, spelling, sva, testthat
SystemRequirements
Enhances
URL	https://github.com/compbiomed/TBSignatureProfiler https://compbiomed.github.io/TBSignatureProfiler-docs/
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_1.10.0.tar.gz
Windows Binary	TBSignatureProfiler_1.10.0.zip
macOS Binary (x86_64)	TBSignatureProfiler_1.10.0.tgz
macOS Binary (arm64)	TBSignatureProfiler_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TBSignatureProfiler
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TBSignatureProfiler
Bioc Package Browser	https://code.bioconductor.org/browse/TBSignatureProfiler/
Package Short Url	https://bioconductor.org/packages/TBSignatureProfiler/
Package Downloads Report	Download Stats