DOI: 10.18129/B9.bioc.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 (3.15)
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.
Author: David Jenkins [aut], Aubrey Odom [aut, cre], Xutao Wang [aut], Yue Zhao [aut], Christian Love [aut], W. Evan Johnson [aut]
Maintainer: Aubrey Odom <aodom at bu.edu>
Citation (from within R,
enter citation("TBSignatureProfiler")
):
Installation
To install this package, start R (version
“4.2”) and enter:
if (!requireNamespace("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 | 1.7.1 |
In Bioconductor since | BioC 3.11 (R-4.0) (1.5 years) |
License | MIT + file LICENSE |
Depends | R (>= 4.1) |
Imports | ASSIGN(>= 1.23.1), GSVA, singscore, methods, ComplexHeatmap, RColorBrewer, ggplot2, S4Vectors, reshape2, ROCit, DESeq2, DT, edgeR, gdata, SummarizedExperiment, magrittr, stats, rlang, BiocParallel, BiocGenerics |
LinkingTo | |
Suggests | testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle, shiny, circlize, caret, dplyr, plyr, impute, sva, glmnet, randomForest, MASS, class, e1071, pROC, HGNChelper |
SystemRequirements | |
Enhances | |
URL | github.com/compbiomed/TBSignatureProfiler compbiomed.github.io/TBSignatureProfiler-docs/ |
BugReports | github.com/compbiomed/TBSignatureProfiler/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Package Archives
Follow
Installation instructions to use this
package in your R session.
Read more here: Source link