TBSignatureProfiler
Profile RNA-Seq Data Using TB Pathway Signatures
Bioconductor version: 3.23 · Package version: 1.24.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TBSignatureProfiler")Details
| Maintainer | Kiloni Quiles <kiloni.quiles@rutgers.edu> |
| Author | Kiloni Quiles [cre] (ORCID: <https://orcid.org/0000-0002-7521-5255>), Aubrey R. Odom [aut, dtm] (ORCID: <https://orcid.org/0000-0001-7113-7598>), David Jenkins [aut, org] (ORCID: <https://orcid.org/0000-0002-7451-4288>), Xutao Wang [aut], Yue Zhao [ctb] (ORCID: <https://orcid.org/0000-0001-5257-5103>), Christian Love [ctb], W. Evan Johnson [aut] |
| License | MIT + file LICENSE |
| URL | https://github.com/wejlab/TBSignatureProfiler, https://wejlab.github.io/TBSignatureProfiler-docs/ |
| Bug Reports | https://github.com/wejlab/TBSignatureProfiler/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, Software |
| Package Short Url | https://bioconductor.org/packages/TBSignatureProfiler/ |
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.
Documentation
Download
Follow the 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 (arm64) | TBSignatureProfiler_1.24.0.tgz |
| macOS binary (x86_64) | TBSignatureProfiler_1.24.0.tgz |
Dependencies
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
Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071, impute, knitr, lintr, MASS, plyr, randomForest, rmarkdown, shiny, spelling, sva, testthat
Reverse dependencies
Suggests Me (1): LegATo