DOI: 10.18129/B9.bioc.TBSignatureProfiler  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler.

Profile RNA-Seq Data Using TB Pathway Signatures

Bioconductor version: 3.17

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-Mabey [aut, cre, dtm] , David Jenkins [aut, org] , Xutao Wang [aut], Yue Zhao [ctb] , Christian Love [ctb], W. Evan Johnson [aut]

Maintainer: Aubrey R. Odom-Mabey <aodom at bu.edu>

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


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HTML R Script Introduction to the TBSignatureProfiler
PDF   Reference Manual


biocViews DifferentialExpression, GeneExpression, Software
Version 1.12.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports ASSIGN(>= 1.23.1), BiocParallel, ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, GSVA, magrittr, methods, RColorBrewer, reshape2, rlang, ROCit, S4Vectors, singscore, stats, SummarizedExperiment
Suggests BiocStyle, caret, circlize, class, covr, dplyr, e1071, glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC, randomForest, rmarkdown, shiny, spelling, sva, testthat
URL https://github.com/compbiomed/TBSignatureProfiler https://compbiomed.github.io/TBSignatureProfiler-docs/
BugReports https://github.com/compbiomed/TBSignatureProfiler/issues
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Source Package TBSignatureProfiler_1.12.0.tar.gz
Windows Binary TBSignatureProfiler_1.12.0.zip
macOS Binary (x86_64) TBSignatureProfiler_1.12.0.tgz
macOS Binary (arm64) TBSignatureProfiler_1.12.0.tgz
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Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TBSignatureProfiler
Bioc Package Browser https://code.bioconductor.org/browse/TBSignatureProfiler/
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