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

Documentation for package ‘BUMHMM’ version 1.11.0

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.