TBSignatureProfiler

DOI: 10.18129/B9.bioc.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 (3.14)

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.

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

Maintainer: Aubrey Odom <aodom at bu.edu>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews DifferentialExpression, GeneExpression, Software
Version 1.5.14
In Bioconductor since BioC 3.11 (R-4.0) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports ASSIGN(>= 1.23.1), GSVA, singscore, methods, ComplexHeatmap, RColorBrewer, ggplot2, S4Vectors, reshape2, ROCit, DESeq2, DT, edgeR, gdata, SummarizedExperiment, magrittr, stats, rlang, BiocParallel, BiocGenerics
LinkingTo
Suggests testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle, shiny, circlize, caret, dplyr, plyr, impute, sva, glmnet, randomForest, MASS, class, e1071, pROC, HGNChelper
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_1.5.14.tar.gz
Windows Binary TBSignatureProfiler_1.5.14.zip (32- & 64-bit)
macOS 10.13 (High Sierra) TBSignatureProfiler_1.5.14.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

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