STADyUM
This is the development version of STADyUM; for the stable release version, see STADyUM.
Statistical Transcriptome Analysis under a Dynamic Unified Model
Bioconductor version: Development (3.24)
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.
Author: Yixin Zhao [aut] 
, Lingjie Liu [aut] , Rebecca Hassett [aut, cre] , Xin Zeng [aut, aut]
Maintainer: Rebecca Hassett <hassett at cshl.edu>
citation("STADyUM")):Yixin Zhao, Lingjie Liu, Rebecca Hassett, Xin Zeng. STADyUM: Statistical Transcriptome Analysis under a Dynamic Unified Model. doi:10.18129/B9.bioc.STADyUM, R package version 1.3.2, https://bioconductor.org/packages/STADyUM.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("STADyUM")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("STADyUM")| Comparative Analysis of Promoter-Proximal Pausing using Likelihood Ratio Tests | HTML | R Script |
| Estimating Transcription Rates with STADyUM from PRO-seq Data | HTML | R Script |
| STADyUM: Simulating and Analyzing Transcription Dynamics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Preprocessing, Sequencing, Software, StatisticalMethod, Transcription, Transcriptomics |
| Version | 1.3.2 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | GenomicRanges, IRanges, S4Vectors, methods, tibble, dplyr, ggplot2, progress, GenomeInfoDb, Rcpp, data.table, purrr, rtracklayer, tidyr, rlang, MASS, plyranges, pracma, ggpointdensity, BiocFileCache |
| System Requirements | |
| URL | https://github.com/rhassett-cshl/STADyUM |
| Bug Reports | https://github.com/rhassett-cshl/STADyUM |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, devtools, ggpubr, cowplot |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | STADyUM_1.3.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | STADyUM_1.3.2.tgz |
| macOS Binary (sonoma-arm64) | STADyUM_1.3.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/STADyUM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/STADyUM |
| Package Short Url | https://bioconductor.org/packages/STADyUM/ |
| Package Downloads Report | Download Stats |