BUMHMM

DOI: 10.18129/B9.bioc.BUMHMM  

Computational pipeline for computing probability of modification from structure probing experiment data

Bioconductor version: Release (3.17)

This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.

Author: Alina Selega (alina.selega@gmail.com), Sander Granneman, Guido Sanguinetti

Maintainer: Alina Selega <alina.selega at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("BUMHMM")

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("BUMHMM")

 

PDF	R Script	An Introduction to the BUMHMM pipeline
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, Classification, Coverage, FeatureExtraction, GeneExpression, GeneRegulation, GeneticVariability, Genetics, HiddenMarkovModel, ImmunoOncology, RNASeq, Regression, Sequencing, Software, StructuralPrediction, Transcription, Transcriptomics
Version	1.24.0
In Bioconductor since	BioC 3.5 (R-3.4) (6.5 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges
LinkingTo
Suggests	testthat, knitr, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	BUMHMM_1.24.0.tar.gz
Windows Binary	BUMHMM_1.24.0.zip
macOS Binary (x86_64)	BUMHMM_1.24.0.tgz
macOS Binary (arm64)	BUMHMM_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BUMHMM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BUMHMM
Bioc Package Browser	https://code.bioconductor.org/browse/BUMHMM/
Package Short Url	https://bioconductor.org/packages/BUMHMM/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive