TBSignatureProfiler

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler.

Profile RNA-Seq Data Using TB Pathway Signatures

DOI: 10.18129/B9.bioc.TBSignatureProfiler

Bioconductor version: 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 (!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")

Introduction to the TBSignatureProfiler HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneExpression, Software

Version 1.6.0

In Bioconductor since BioC 3.11 (R-4.0) (4 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

System Requirements

URL https://github.com/compbiomed/TBSignatureProfiler https://compbiomed.github.io/TBSignatureProfiler-docs/

Bug Reports https://github.com/compbiomed/TBSignatureProfiler/issues

Suggests testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle, shiny, circlize, caret, dplyr, plyr, impute, sva, glmnet, randomForest, MASS, class, e1071, pROC, HGNChelper

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