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

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Documentation for package ‘BUMHMM’ version 1.29.0

• 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.