STADyUM
Statistical Transcriptome Analysis under a Dynamic Unified Model
Bioconductor version: 3.23 · Package version: 1.2.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
STADyUM is a package with functionality for analyzing nascent RNA read counts to infer transcription rates. This includes utilities for processing experimental nascent RNA read counts as well as for simulating PRO-seq data. Rates such as initiation, pause release and landing pad occupancy are estimated from either synthetic or experimental data. There are also options for varying pause sites and including steric hindrance of initiation in the model.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("STADyUM")Details
| Maintainer | Rebecca Hassett <hassett@cshl.edu> |
| Author | Yixin Zhao [aut] (ORCID: <https://orcid.org/0000-0002-7856-2818>), Lingjie Liu [aut] (ORCID: <https://orcid.org/0000-0002-5765-1213>), Rebecca Hassett [aut, cre] (ORCID: <https://orcid.org/0000-0001-5133-9387>) |
| License | MIT + file LICENSE |
| URL | https://github.com/rhassett-cshl/STADyUM |
| Bug Reports | https://github.com/rhassett-cshl/STADyUM |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Sequencing, Software, StatisticalMethod, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/STADyUM/ |
Citation
From within R, enter citation("STADyUM"):
Yixin Zhao, Lingjie Liu, Rebecca Hassett. STADyUM: Statistical Transcriptome Analysis under a Dynamic Unified Model. doi:10.18129/B9.bioc.STADyUM, R package version 1.2.0, https://bioconductor.org/packages/STADyUM.
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 | STADyUM_1.2.0.tar.gz |
| Windows binary (x86_64) | STADyUM_1.1.3.zip |
| macOS binary (arm64) | STADyUM_1.2.0.tgz |
| macOS binary (x86_64) | STADyUM_1.2.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: GenomicRanges, IRanges, S4Vectors, methods, tibble, dplyr, ggplot2, progress, GenomeInfoDb, Rcpp, data.table, purrr, rtracklayer, tidyr, rlang, MASS
LinkingTo: Rcpp
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, devtools