TBSignatureProfiler

This package is for version 3.21 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: 3.21

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] ORCID iD ORCID: 0000-0001-7113-7598 , David Jenkins [aut, org] ORCID iD ORCID: 0000-0002-7451-4288 , Xutao Wang [aut], Yue Zhao [ctb] ORCID iD ORCID: 0000-0001-5257-5103 , 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 "4.5") 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

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneExpression, Software

Version 1.20.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 years)

License MIT + file LICENSE

Depends R (>= 4.4.0)

Imports ASSIGN(>= 1.23.1), BiocParallel, ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, glmnet, GSVA(>= 1.51.3), HGNChelper, magrittr, methods, pROC, RColorBrewer, reshape2, ROCit, S4Vectors, singscore, stats, SummarizedExperiment, tibble

System Requirements

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

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

Suggests BiocStyle, caret, circlize, class, covr, dplyr, e1071, impute, knitr, lintr, MASS, plyr, 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_1.20.0.tar.gz

Windows Binary (x86_64) TBSignatureProfiler_1.20.0.zip

macOS Binary (x86_64) TBSignatureProfiler_1.20.0.tgz

macOS Binary (arm64) TBSignatureProfiler_1.20.0.tgz

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/

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