EBSeqHMM

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see EBSeqHMM.

Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments


Bioconductor version: 3.15

The EBSeqHMM package implements an auto-regressive hidden Markov model for statistical analysis in ordered RNA-seq experiments (e.g. time course or spatial course data). The EBSeqHMM package provides functions to identify genes and isoforms that have non-constant expression profile over the time points/positions, and cluster them into expression paths.

Author: Ning Leng, Christina Kendziorski

Maintainer: Ning Leng <lengning1 at gmail.com>

Citation (from within R, enter citation("EBSeqHMM")):

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EBSeqHMM")

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("EBSeqHMM")
HMM PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, DifferentialExpression, GeneExpression, HiddenMarkovModel, ImmunoOncology, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, TimeCourse
Version 1.30.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic-2.0
Depends EBSeq
Imports
System Requirements
URL
See More
Suggests
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package EBSeqHMM_1.30.0.tar.gz
Windows Binary EBSeqHMM_1.30.0.zip
macOS Binary (x86_64) EBSeqHMM_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EBSeqHMM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EBSeqHMM
Bioc Package Browser https://code.bioconductor.org/browse/EBSeqHMM/
Package Short Url https://bioconductor.org/packages/EBSeqHMM/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive