BUMHMM
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see BUMHMM.
Computational pipeline for computing probability of modification from structure probing experiment data
Bioconductor version: 3.11
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("BUMHMM")):
Installation
To install this package, start R (version "4.0") 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")| An Introduction to the BUMHMM pipeline | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Classification, Coverage, FeatureExtraction, GeneExpression, GeneRegulation, GeneticVariability, Genetics, HiddenMarkovModel, ImmunoOncology, RNASeq, Regression, Sequencing, Software, StructuralPrediction, Transcription, Transcriptomics |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | GPL-3 |
| Depends | R (>= 3.4) |
| Imports | devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges |
| System Requirements | |
| URL |
See More
| Suggests | testthat, knitr, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BUMHMM_1.12.0.tar.gz |
| Windows Binary | BUMHMM_1.12.0.zip |
| macOS 10.13 (High Sierra) | BUMHMM_1.12.0.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 3.11 | Source Archive |