Man pages for lbroseus/SIRFindeR
More stable and accurate estimation of Intron Retention levels
| appendIntronicCounts | Internal function appendIntronicCounts() |
| bootstrapJunctionCounts | Internal function bootstrapJunctionCounts() |
| bootstrapMean | Internal function bootstrapMean() |
| bootstrapSample | Internal function bootstrapSample() |
| buildExpSIRmatrix | Combine all SIRratio values in a same matrix. |
| callIRevents | Call Intron Retention events from RNA long read alignments |
| computeIRrates | Compute observed IR rates from a Long Read experiment |
| computeRegionOverlap | Compute the fraction of an intron contained in a long read |
| computeSIRratio | Intron retention levels estimation using short read RNA-seq... |
| createIntronGR | Deduce independent intron intervals from a transcriptome... |
| curateIntrons | Internal function for excluding low mappability regions from... |
| defineIntronicIntervals | Internal function to define sample-specific intronic... |
| estimateSIRratio | Internal function to estimate the SIRratio |
| liftItOver | Internal function for genome liftover |
| mergebyIntron | Merging SIRratio by reference independent intron. |
| mergeJunctionFiles | Internal function for merging introns detected by STAR |
| prepareJunctionSites | Internal function for extracting junction counts from a STAR... |
| prepareSIRmatrix | Prepare a matrix of SIRratio values for usual primary... |
