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EBSeqHMM

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


Bioconductor version: Release (3.18)

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 "4.3") 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 1.35.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License Artistic-2.0
Depends EBSeq
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Package Archives

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

Source Package EBSeqHMM_1.35.0.tar.gz
Windows Binary EBSeqHMM_1.35.0.zip
macOS Binary (x86_64) EBSeqHMM_1.35.0.tgz
macOS Binary (arm64) EBSeqHMM_1.35.0.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/
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