TBSignatureProfiler

DOI: 10.18129/B9.bioc.TBSignatureProfiler    

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

Profile RA-Seq Data Using TB Pathway Signatures

Bioconductor version: Development (3.12)

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>

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

Installation

To install this package, start R (version "4.0") 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 1.1.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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_1.1.0.tar.gz
Windows Binary TBSignatureProfiler_1.1.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) TBSignatureProfiler_1.1.0.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

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