EBSeqHMM

DOI: 10.18129/B9.bioc.EBSeqHMM    

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

Bioconductor version: Release (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>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("EBSeqHMM", version = "3.8")

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, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, TimeCourse
Version 1.16.0
In Bioconductor since BioC 3.0 (R-3.1) (4 years)
License Artistic-2.0
Depends EBSeq
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package EBSeqHMM_1.16.0.tar.gz
Windows Binary EBSeqHMM_1.16.0.zip
Mac OS X 10.11 (El Capitan) EBSeqHMM_1.16.0.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/
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