Man pages for mikelove/alpine
alpine
| alpine-package | alpine: bias corrected transcript abundance estimation |
| buildFragtypes | Build fragment types from exons |
| estimateAbundance | Estimate bias-corrected transcript abundances (FPKM) |
| estimateTheta | Estimate bias-corrected transcript abundances (FPKM) |
| extractAlpine | Extract results from estimateAbundance run across genes |
| fitBiasModels | Fit bias models over single-isoform genes |
| 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)... |
| plotRelPos | Plot relative position bias over samples |
| predictCoverage | Predict coverage for a single-isoform gene |
| preprocessedData | Preprocessed data for vignettes and examples |
| splitGenesAcrossChroms | Split genes that have isoforms across chromosomes |
| splitLongGenes | Split very long genes |
