TBSignatureProfiler
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler.
Profile RNA-Seq Data Using TB Pathway Signatures
Bioconductor version: 3.19
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] 
, David Jenkins [aut, org] , Xutao Wang [aut], Yue Zhao [ctb] , Christian Love [ctb], W. Evan Johnson [aut]
Maintainer: Aubrey R. Odom <aodom at bu.edu>
citation("TBSignatureProfiler")):
Installation
To install this package, start R (version "4.4") 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 | ||
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.2.0) |
| Imports | ASSIGN(>= 1.23.1), BiocParallel, ComplexHeatmap, DESeq2, DT, edgeR, gdata, ggplot2, GSVA(>= 1.51.3), magrittr, methods, RColorBrewer, reshape2, rlang, ROCit, S4Vectors, singscore, stats, SummarizedExperiment |
| 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, glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC, randomForest, rmarkdown, shiny, spelling, sva, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TBSignatureProfiler_1.16.0.tar.gz |
| Windows Binary (x86_64) | TBSignatureProfiler_1.16.0.zip (64-bit only) |
| macOS Binary (x86_64) | TBSignatureProfiler_1.16.0.tgz |
| macOS Binary (arm64) | TBSignatureProfiler_1.16.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |