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Bioconductor - BUMHMM (development version)

BUMHMM

This is the development version of BUMHMM; for the stable release version, see BUMHMM.

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

Bioconductor version: Development (3.22)

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>

Citation (from within R, enter citation("BUMHMM")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews Bayesian, Classification, Coverage, FeatureExtraction, GeneExpression, GeneRegulation, GeneticVariability, Genetics, HiddenMarkovModel, ImmunoOncology, RNASeq, Regression, Sequencing, Software, StructuralPrediction, Transcription, Transcriptomics Version 1.33.0 In Bioconductor since BioC 3.5 (R-3.4) (8 years) License GPL-3 Depends R (>= 3.5.0) Imports devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges System Requirements URL See More Package Archives

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

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