TBSignatureProfiler

This is the released version of TBSignatureProfiler; for the devel version, see TBSignatureProfiler.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

Profile RNA-Seq Data Using TB Pathway Signatures

Bioconductor version: Release (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: 0000-0002-7521-5255 , Aubrey R. Odom [aut, 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: Kiloni Quiles <kiloni.quiles at rutgers.edu>

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

Aubrey R. Odom, David Jenkins, Xutao Wang, W. Evan Johnson. TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures. doi:10.18129/B9.bioc.TBSignatureProfiler, R package version 1.24.0, https://bioconductor.org/packages/TBSignatureProfiler.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.24.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	LegATo
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	TBSignatureProfiler_1.24.0.tar.gz
Windows Binary (x86_64)	TBSignatureProfiler_1.24.0.zip
macOS Binary (big-sur-x86_64)	TBSignatureProfiler_1.24.0.tgz
macOS Binary (sonoma-arm64)	TBSignatureProfiler_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TBSignatureProfiler
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TBSignatureProfiler
Package Short Url	https://bioconductor.org/packages/TBSignatureProfiler/
Package Downloads Report	Download Stats