alpine-package | alpine: bias corrected transcript abundance estimation |
buildFragtypes | Build fragment types from exons |
ebt.fit | Preprocessed data for vignettes and examples |
ebt.theta | Preprocessed data for vignettes and examples |
estimateAbundance | Estimate bias-corrected transcript abundances (FPKM) |
extractAlpine | Extract results from estimateAbundance run across genes |
fitBiasModels | Fit bias models over single-isoform genes |
fitpar | Preprocessed data for vignettes and examples |
fitpar.small | Preprocessed data for vignettes and examples |
genes.theta | Preprocessed data for vignettes and examples |
getFragmentWidths | Get fragment widths |
getReadLength | Get read length |
mergeGenes | Merge overlapping "genes" into gene clusters |
normalizeDESeq | DESeq median ratio normalization for matrix |
plotFragLen | Plot fragment length distribution over samples |
plotGC | Plot the fragment GC bias over samples |
plotGRL | Simple segments plot for GRangesList |
plotOrder0 | Plot parameters of the variable length Markov model (VLMM) for read starts |
plotOrder1 | Plot parameters of the variable length Markov model (VLMM) for read starts |
plotOrder2 | Plot parameters of the variable length Markov model (VLMM) for read starts |
plotRelPos | Plot relative position bias over samples |
predictCoverage | Predict coverage for a single-isoform gene |
preprocessedData | Preprocessed data for vignettes and examples |
res | Preprocessed data for vignettes and examples |
splitGenesAcrossChroms | Split genes that have isoforms across chromosomes |
splitLongGenes | Split very long genes |
txdf.theta | Preprocessed data for vignettes and examples |