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

## Documentation for package ‘BUMHMM’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

computeProbs | Function to compute posterior probabilities of modification with the BUM-HMM model for all nucleotides.
computeStretches | Function to compute continuous stretches of nucleotide positions.
covFile | Example coverage data set.
docFile | Example drop-off count data set.
dorFile | Example drop-off rate data set.
findPatternPos | Function to find positions of the nucleotide patterns in the sequence.
nuclPerm | Function to create nucleobase patterns.
scaleDOR | Function to scale drop-off rates across replicates to a common median.
se | Example RNA structure probing data set.
selectNuclPos | Function to compute selections of nucleotide positions.
seq | Example genomic sequence string.
stabiliseVariance | Function to reduce variance of LDRs as a function of coverage.