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biocLite("EBSeqHMM")
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EBSeqHMM
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bioconductor version: 3.0
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 <nleng at wisc.edu>
Citation (from within R,
enter citation("EBSeqHMM")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("EBSeqHMM")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("EBSeqHMM")
| R Script | HMM | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bayesian, DifferentialExpression, GeneExpression, HiddenMarkovModel, MultipleComparison, RNASeq, Sequencing, Software, StatisticalMethod, TimeCourse |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | EBSeq |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | EBSeqHMM_1.0.0.tar.gz |
| Windows Binary | EBSeqHMM_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | EBSeqHMM_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | EBSeqHMM_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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