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TBSignatureProfiler

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

Profile RNA-Seq Data Using TB Pathway Signatures


Bioconductor version: Development (3.19)

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 [aut, cre, dtm] , David Jenkins [aut, org] , Xutao Wang [aut], Yue Zhao [ctb] , Christian Love [ctb], W. Evan Johnson [aut]

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

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DifferentialExpression, GeneExpression, Software
Version 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports ASSIGN(>= 1.23.1), BiocParallel, ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, GSVA, magrittr, methods, RColorBrewer, reshape2, rlang, ROCit, S4Vectors, singscore, stats, SummarizedExperiment
System Requirements
URL https://github.com/compbiomed/TBSignatureProfiler https://compbiomed.github.io/TBSignatureProfiler-docs/
Bug Reports https://github.com/compbiomed/TBSignatureProfiler/issues
See More
Suggests BiocStyle, caret, circlize, class, covr, dplyr, e1071, glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC, randomForest, rmarkdown, shiny, spelling, sva, testthat
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Package Archives

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

Source Package TBSignatureProfiler_1.15.0.tar.gz
Windows Binary TBSignatureProfiler_1.15.0.zip
macOS Binary (x86_64) TBSignatureProfiler_1.15.0.tgz
macOS Binary (arm64)
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