Package: BUMHMM
Type: Package
Title: Computational pipeline for computing probability of modification
        from structure probing experiment data
Version: 1.34.0
Date: 2021-11-20
Author: Alina Selega (alina.selega@gmail.com), Sander Granneman, Guido
        Sanguinetti
Maintainer: Alina Selega <alina.selega@gmail.com>
Description: 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.
Depends: R (>= 3.5.0)
License: GPL-3
Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment,
        Biostrings, IRanges
Suggests: testthat, knitr, BiocStyle
VignetteBuilder: knitr
LazyData: true
biocViews: ImmunoOncology, GeneticVariability, Transcription,
        GeneExpression, GeneRegulation, Coverage, Genetics,
        StructuralPrediction, Transcriptomics, Bayesian,
        Classification, FeatureExtraction, HiddenMarkovModel,
        Regression, RNASeq, Sequencing
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libfribidi-dev
        git make libharfbuzz-dev libgit2-dev libicu-dev libjpeg-dev
        libpng-dev libtiff-dev libwebp-dev libxml2-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:35:55 UTC
RemoteUrl: https://github.com/bioc/BUMHMM
RemoteRef: RELEASE_3_22
RemoteSha: 63f1678d0746bb302df7ef66c5855b5865e059de
NeedsCompilation: no
Packaged: 2025-11-11 13:30:40 UTC; root
Built: R 4.5.2; ; 2025-11-11 13:35:08 UTC; windows
