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. |