API for fmicompbio/QuasR
Quantify and Annotate Short Reads in R
| Global functions | |
|---|---|
| .get_alnstats_for_bam | Man page Source code |
| .qa_ShortRead | Source code |
| BSgenomeSeqToFasta | Source code |
| QuasR | Man page |
| QuasR-package | Man page |
| [,qProject,ANY,missing,missing-method | Man page |
| addNumericToID | Source code |
| align_Rbowtie | Source code |
| align_RbowtieCtoT_dir | Source code |
| align_RbowtieCtoT_undir | Source code |
| align_RbowtieSpliced | Source code |
| align_Rhisat2 | Source code |
| alignmentStats | Man page Source code |
| alignments | Man page |
| alignments,qProject-method | Man page |
| auxiliaries | Man page |
| auxiliaries,qProject-method | Man page |
| bamInfoOnlyBaseName | Source code |
| buildIndex | Source code |
| buildIndexPackage | Source code |
| buildIndexSNP | Source code |
| buildIndex_Rbowtie | Source code |
| buildIndex_RbowtieCs | Source code |
| buildIndex_RbowtieCtoT | Source code |
| buildIndex_Rhisat2 | Source code |
| buildSpliceSiteFile | Source code |
| calcMmInformation | Source code |
| calcQaInformation | Source code |
| class:qProject | Man page |
| compressFile | Source code |
| compressedFileFormat | Source code |
| consolidateFileExtensions | Source code |
| countAlignments | Source code |
| countJunctionsOneBamfile | Source code |
| createAuxAlignments | Source code |
| createAuxAlignmentsController | Source code |
| createGenomicAlignments | Source code |
| createGenomicAlignmentsController | Source code |
| createQProject | Source code |
| createReferenceSequenceIndices | Source code |
| createSeedList | Source code |
| detectVariantsBamfilesRegionsSingleChromosome | Source code |
| determineSamplesFormat | Source code |
| displayNames | Source code |
| filterLength | Source code |
| filterLowComplexity | Source code |
| freeDiskSpace | Source code |
| genome,qProject-method | Man page |
| getListOfBiocParallelParam | Source code |
| length,qProject-method | Man page |
| loadQuasR | Source code |
| md5subsum | Source code |
| missingFilesMessage | Source code |
| pathAsAbsoluteRedirected | Source code |
| plotDuplicated | Source code |
| plotErrorsByCycle | Source code |
| plotFragmentDistribution | Source code |
| plotMappings | Source code |
| plotMismatchTypes | Source code |
| plotNuclByCycle | Source code |
| plotQualByCycle | Source code |
| plotUniqueness | Source code |
| preprocessPairedReads | Source code |
| preprocessReads | Man page Source code |
| preprocessSingleReads | Source code |
| profileAlignments | Source code |
| qAlign | Man page Source code |
| qCount | Man page Source code |
| qExportWig | Man page Source code |
| qMeth | Man page Source code |
| qProfile | Man page Source code |
| qProject | Man page |
| qProject-class | Man page |
| qProjectBamInfo | Source code |
| qProjectUpdate | Man page Source code |
| qQCReport | Man page Source code |
| quantifyMethylationBamfilesRegionsSingleChromosome | Source code |
| quantifyMethylationBamfilesRegionsSingleChromosomeAllele | Source code |
| quantifyMethylationBamfilesRegionsSingleChromosomeSingleAlignmen | Source code |
| resolveCacheDir | Source code |
| samToSortedBamCore | Source code |
| samToSortedBamParallel | Source code |
| show,qProject-method | Man page |
| truncPath | Source code |
| truncString | Source code |
| truncStringToPlotWidth | Source code |
| worker_message | Man page Source code |
