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STADyUM
This is thedevelopment version of STADyUM; for the stable release version, seeSTADyUM.
Statistical Transcriptome Analysis under a Dynamic Unified Model
Bioconductor version: Development (3.23)
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]
ORCID: 0000-0002-7856-2818, Lingjie Liu [aut] ORCID: 0000-0002-5765-1213, Rebecca Hassett [aut, cre] ORCID: 0000-0001-5133-9387
Maintainer: Rebecca Hassett <hassett at cshl.edu>
citation("STADyUM")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("STADyUM")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("STADyUM")| STADyUM: Simulating and Analyzing Transcription Dynamics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Sequencing,Software,StatisticalMethod,Transcription,Transcriptomics |
| Version | 1.1.3 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | MIT + fileLICENSE |
| Depends | R (>= 4.5.0) |
| Imports | GenomicRanges,IRanges,S4Vectors, methods,tibble,dplyr,ggplot2,progress,GenomeInfoDb,Rcpp,data.table,purrr,rtracklayer,tidyr,rlang,MASS |
| 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 |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | STADyUM_1.1.3.tar.gz |
| Windows Binary (x86_64) | STADyUM_1.1.3.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | STADyUM_1.1.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/STADyUM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/STADyUM |
| Bioc Package Browser | https://code.bioconductor.org/browse/STADyUM/ |
| Package Short Url | https://bioconductor.org/packages/STADyUM/ |
| Package Downloads Report | Download Stats |