TBSignatureProfiler

This is the development version of TBSignatureProfiler; for the stable release version, see TBSignatureProfiler.

Profile RNA-Seq Data Using TB Pathway Signatures

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DOI: 10.18129/B9.bioc.TBSignatureProfiler

Bioconductor version: Development (3.23)

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: Kiloni Quiles [cre] ORCID iD ORCID: 0000-0002-7521-5255 , Aubrey R. Odom [aut, 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: Kiloni Quiles <kiloni.quiles at rutgers.edu>

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

Installation

To install this package, start R (version "4.6") 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.