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Bioconductor - TBSignatureProfiler (development version)

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 (3.22)

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

# 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 1.21.1 In Bioconductor since BioC 3.11 (R-4.0) (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 See More Suggests BiocStyle, caret, circlize, class, covr, dplyr, e1071, impute, knitr, lintr, MASS, plyr, randomForest, rmarkdown, shiny, spelling, sva, testthat Linking To Enhances Depends On Me Imports Me Suggests Me LegATo Links To Me Build Report Build Report Package Archives

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

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