EBSeqHMM

DOI: 10.18129/B9.bioc.EBSeqHMM    

This package is for version 3.8 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: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	HMM
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, DifferentialExpression, GeneExpression, HiddenMarkovModel, ImmunoOncology, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, TimeCourse
Version	1.16.1
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 years)
License	Artistic-2.0
Depends	EBSeq
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Build Report

Package Archives

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

Source Package	EBSeqHMM_1.16.1.tar.gz
Windows Binary	EBSeqHMM_1.16.1.zip
Mac OS X 10.11 (El Capitan)	EBSeqHMM_1.16.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EBSeqHMM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EBSeqHMM
Package Short Url	http://bioconductor.org/packages/EBSeqHMM/
Package Downloads Report	Download Stats