Bioconductor – TBSignatureProfiler (development version)

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 (3.15)

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
“4.2”) 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")

 

Details

biocViews DifferentialExpression, GeneExpression, Software
Version 1.7.1
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 github.com/compbiomed/TBSignatureProfiler compbiomed.github.io/TBSignatureProfiler-docs/
BugReports github.com/compbiomed/TBSignatureProfiler/issues
Depends On Me
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Build Report  

Package Archives

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


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