Man pages for BMILAB/movAPA
movAPA: Modeling and Visualization of Dynamics of Alternative PolyAdenylation
| annotateByKnownPAC | Annotate a PACdataset with known PACdatasets |
| annotateByPAS | Annotate a PACdataset with polyA signals |
| annotatePAC | Annotate PACs |
| asAnyMatrix | Convert to matrix or dgCMatrix |
| buildRefPACdsAnno | Build a reference annotation of PACdataset |
| countOvpPACds | Count overlapping between PACdatasets |
| createPACdataset | Create a PACdataset from counts data |
| demo_peaks | A demo peaks list of human |
| ext3UTRPACds | Extend 3'UTR |
| faFromPACds | Extract sequences from a PACdataset. |
| findOvpPACds | Find overlapping PACdataset |
| get3UTRAPAds | Get 3'UTR APA PACdataset |
| get3UTRAPApd | Get proximal and distal 3'UTR APAs |
| getNearbyPAdist | Get distance between nearby pAs |
| getVarGrams | Get actual grams for an abbreviation |
| heatmapResults-class | heatmapResult object |
| kcount | Count kgrams |
| length | Length of a PACdataset |
| makeExamplePACds | Make an example PACdataset |
| mergePACds | Merge multiple PACdatasets |
| mergePACds_v0 | Merge multiple PACdatasets for RNA-seq |
| movAPAindex | Get APA index |
| movAPAindexDiff | Get APA index difference between conditions |
| movAPA-package | movAPA: movAPA: Modeling and Visualization of Dynamics of... |
| movAPAswitch | Analyze APA site switching. |
| movAPASwitchRes-class | movAPASwitchRes object |
| movDEGene | Get DE genes |
| movDEGeneRes-class | movDEGeneRes object |
| movDEPAC | Get DE PACs |
| movDEPACRes-class | movDEPACRes object |
| movIndexDiffRes-class | movIndexDiffRes object |
| movPAindex | Calculate PAC index for each PAC in each condition. |
| movRes2heatmapResults | Convert movRes object to heatmapResults object |
| movRes-class | movRes object |
| movSelect | Select movRes |
| movStat | Make statistics for a object |
| movUTRtrend | Analyze 3' UTR shortening/lengthening. |
| movUTRTrendRes-class | movUTRTrendRes object |
| movViz | movViz generic |
| movVizSC | Visualize PACs of a gene in single cells |
| normalizePACds | Normalize a PACdataset |
| outputHeatStat | Output movStat results |
| PACdataset-class | PACdataset object |
| PACds | A demo PACdataset of rice tissues |
| parseGenomeAnnotation | Parse genome annotation |
| parseGff | Parse gff3/gtf genome annotation |
| parseTxdb | Parse TxDb genome annotation |
| plotATCGforFAfile | Plot single nucleotide profile |
| plotCummPAindex | Plot distribution of PA index among biological samples. |
| plotHeatmap | Plot heatmap. |
| plotPACdsStat | Plot movStat results |
| plotSeqLogo | Plot seqlogo for poly(A) signals. |
| rbind | Combine multiple PACdatasets by rows |
| readDESeqDs | Read a DESeqDataset |
| readPACds | Read a PACdataset |
| removePACdsIP | Remove internal priming. |
| samplePACds | Sample a PACdataset |
| scPACds | A demo PACdataset of mouse sperm cells |
| subscript_operator | Subset rows and/or columns of a PACdataset |
| subsetHeatmap | Subset heatmapResults object |
| subsetPACds | Subset a PACdataset |
| summary | Summary of a PACdataset |
| testExt3UTR | Test extended 3'UTR length |
| writePACds | Write a PACdataset into a file |
