TBSignatureProfiler
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler.
Profile RA-Seq Data Using TB Pathway Signatures
Bioconductor version: 3.11
Signatures of TB progression, TB disease, and other TB disease states have been created. This package makes it easy to profile RNA-Seq data using these signatures and common signature profiling tools including ASSIGN, GSVA, and ssGSEA.
Author: David Jenkins [aut, cre], Yue Zhao [aut], W. Evan Johnson [aut], Aubrey Odom [aut], Christian Love [aut]
Maintainer: David Jenkins <dfj at bu.edu>
citation("TBSignatureProfiler")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0.0) |
| Imports | ASSIGN(>= 1.23.1), GSVA, SummarizedExperiment, S4Vectors, methods, BiocParallel, ComplexHeatmap, RColorBrewer, ggplot2, reshape2, circlize, glmnet, ROCit, bioDist, readr, boot, DESeq2, caret, ggfortify, e1071, DT, edgeR, singscore, gdata, shiny |
| System Requirements | |
| URL | https://github.com/compbiomed/TBSignatureProfiler |
| Bug Reports | https://github.com/compbiomed/TBSignatureProfiler/issues |
See More
| Suggests | testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle |
| 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_1.0.0.tar.gz |
| Windows Binary | TBSignatureProfiler_1.0.0.zip |
| macOS 10.13 (High Sierra) | TBSignatureProfiler_1.0.0.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 3.11 | Source Archive |