API for frenkiboy/MyLib
| Global functions | |
|---|---|
| .BigPeakSplitter | Source code |
| .CountNormGenome | Source code |
| .ExportCoverageChr | Source code |
| .First | Source code |
| .FlatPeaksCenter | Source code |
| .ListFiller | Source code |
| .containedIntervals | Source code Source code |
| .get_Region_Annotation | Source code |
| .overlappingIntervals | Source code Source code |
| .test_Functions_Pubmed.R | Source code |
| Alevin_To_Seurat | Source code |
| AnnotateRegionPWM | Source code |
| AnnotateRegions | Source code |
| Annotate_Bamfiles | Source code |
| Annotate_Divergent_Convergent | Source code |
| Annotate_Peaks | Source code |
| Annotate_Reads | Source code |
| Assigner | Source code |
| BEDCoverageToDataFrame | Source code |
| BamIndex | Source code |
| BamName | Source code |
| BamReader | Source code |
| BamReaderChr | Source code |
| BamSelectBed | Source code |
| BamSort | Source code |
| BamToBedGraph | Source code |
| BamToGRanges | Source code |
| BamWindowerChr | Source code |
| BedToGRanges | Source code |
| BigFeatureOverlapBED | Source code |
| BigFeatureOverlapBED.para | Source code |
| BigToRleLoader | Source code |
| Blat | Source code |
| BlocksToPFM | Source code Source code |
| Cell_Cycle_Scoring | Source code |
| CharList2DF | Source code |
| Check_Seurat | Source code |
| ChipSeqRangeUnion | Source code |
| ChrFilter | Source code |
| CisgenomeReader | Source code |
| ClustalO | Source code |
| Colnamer | Source code |
| CombineCoverage | Source code |
| CountOverlaps | Source code |
| CpGDesignator | Source code |
| Creator | Source code |
| DESeq_Results | Source code |
| DGE.fisher | Source code Source code |
| DGE.sig | Source code Source code |
| DGE.sig.cum | Source code Source code |
| DateNamer | Source code |
| Dater | Source code |
| DefineRegionBorders | Source code |
| Designator | Source code |
| DrawHeatmapClusters | Source code |
| Enrichr_all | Source code |
| EnsemblExonsTOGtf | Source code |
| ExportCoverage | Source code |
| ExportReader | Source code |
| ExportToRdata | Source code |
| FindAllMarkersIntersection | Source code |
| FormatEnsembl | Source code |
| GCoords | Source code |
| GRangesToBed | Source code |
| GRangesToBigWig | Source code |
| GRangesTodata.frame | Source code |
| GTFGetAnnotation | Source code |
| GappedBamReader | Source code |
| GenomeLoader | Source code Source code |
| GenomicRegionMaker | Source code |
| GetAnnotOverlaps | Source code |
| GetColors | Source code |
| GetFolds | Source code |
| GetMappingStats | Source code |
| GetOverlaps | Source code Source code |
| GetReads | Source code |
| GetRegs | Source code |
| GetTrimmingStats | Source code |
| Get_Affy_Annotation | Source code |
| GffToBed | Source code |
| GtfSelectTranscript | Source code |
| HexamerCorrectionCalculate | Source code |
| HugeFileLoader | Source code |
| Imprint_Scoring | Source code |
| MakeBinaryContrasts | Source code |
| MakeGeneModels | Source code |
| MakeSlidingWindows | Source code |
| MakeTillingWindows | Source code |
| MapQualFilter | Source code |
| MappingStats_Bowtie | Source code |
| MappingStats_Bowtie2 | Source code |
| MappingStats_SALMON | Source code |
| MappingStats_STAR | Source code |
| MarkovBackground | Source code |
| MatchPWM.Large | Source code |
| MemeBlocks | Source code |
| MemeParser | Source code |
| MergeDataTable | Source code |
| MotifHeatmap | Source code |
| NearEdgeReadRemover | Source code |
| PFMparser | Source code Source code |
| PFMtoPSSM | Source code |
| PFMtoPWM | Source code |
| PSSM.Wasserman.Sandelin | Source code |
| PWMScore | Source code |
| Paraclu | Source code |
| ParseFeatures | Source code |
| ParseGenbank | Source code |
| ParseSequence | Source code |
| Parse_MogeneGEO | Source code |
| PeakFinder | Source code |
| PeakRegionMaker | Source code |
| PeakRegionsToFasta | Source code |
| PeakScoreToRank | Source code |
| Percentager | Source code |
| PlotClusters | Source code |
| PlotPCA | Source code |
| Process_Seurat | Source code |
| RandomRemover | Source code |
| ReadAlevin | Source code |
| ReadAlignedBedFilter | Source code |
| ReadGTFAnnotation | Source code |
| ReadQualFilter | Source code |
| ReadQualFinder | Source code |
| RegionCleaner | Source code |
| RegionCorrector | Source code |
| RepeatMaskerToGRanges | Source code |
| Reverse_Complement_Matrix | Source code |
| Reverse_Complement_Model | Source code |
| Sample_FindRegion | Source code |
| ScanPWM | Source code |
| SetOverlapFinder | Source code |
| Seurat_Meta_Counts | Source code |
| SeurateToSingleCellExperiment | Source code |
| StandardChipseqLoader | Source code |
| Subset_Genes_Seurat | Source code |
| Subset_Seurat | Source code |
| Summarize_Motif_Hits | Source code |
| SwemblReader | Source code |
| TillingWindow | Source code |
| TillingWindowMax | Source code |
| TrimmingStats_BBduk | Source code |
| UCSC.hg.ChrCleaner | Source code |
| UCSC2Reader | Source code |
| UCSCEnsReader | Source code |
| UCSCRefReader | Source code |
| Uniquer | Source code |
| WriteAbstract | Source code |
| WriteBed | Source code |
| WriteRegs | Source code |
| WriteRegsToBed | Source code |
| Zscore | Source code |
| addLetter | Source code |
| annotateDECOD | Source code |
| annotate_Antisense | Source code |
| annotate_Refseq | Source code |
| annotate_deepbind | Source code |
| annotate_tomtom | Source code |
| bed.to.genomeInt | Source code |
| bed.to.genomeInt.strand | Source code |
| cacheFile | Source code Source code |
| calculate_kmers | Source code |
| call_MACS2 | Source code |
| center | Source code |
| check_DNAStringSet_Name | Source code Source code |
| chrFinder | Source code |
| chrSeqlevels | Source code |
| chrStats | Source code |
| clusterFeaturesBED | Source code Source code |
| clusterFeaturesBED.sinfo | Source code |
| clustergram | Source code |
| collect.garbage | Source code Source code |
| combine_Enrichr | Source code |
| compare_Clusters | Source code |
| convertToBED | Source code Source code |
| copy_Private | Source code |
| copy_Public | Source code |
| copy_Public_DT | Source code |
| copy_Public_rds | Source code |
| corrRemover | Source code |
| define_Clusters | Source code Source code |
| diffAll | Source code Source code |
| diffCol | Source code Source code |
| diffMark | Source code Source code |
| diffNum | Source code Source code |
| diffSel | Source code Source code |
| diffTab | Source code Source code |
| difflog | Source code |
| dtfindOverlaps | Source code |
| extract_Jaspar_Motifs | Source code |
| featureContainBED.strand | Source code Source code |
| featureOverlapBED | Source code Source code |
| featureOverlapBED.para | Source code Source code |
| featureOverlapBED.strand | Source code Source code |
| featureOverlapBED.strand.para | Source code Source code |
| fetchAnnotation | Source code |
| fetchGoogleSheet | Source code |
| fetch_Abstract | Source code |
| fetch_SampleSheet | Source code |
| file_Copy | Source code |
| filterCluster | Source code |
| findRegions | Source code |
| findRegionsGenome | Source code |
| findRegionsRLE | Source code |
| find_Motif_Hits | Source code |
| find_enriched_kmer_regions | Source code |
| flipStrand | Source code |
| g.int.clusterBED | Source code |
| g.int.clusterBED.strand | Source code |
| g.int.intersectBED | Source code |
| g.int.nonoverlapBED | Source code |
| g.int.overlapBED | Source code |
| g.int.overlapBED.list | Source code |
| genomeInt.to.bed | Source code |
| genomeInt.to.bed.strand | Source code |
| getMeans | Source code |
| getMeans.DESeqDataSet | Source code |
| getMeans.VST | Source code |
| getResults | Source code |
| getResults_limma | Source code |
| get_DifferentialExpression | Source code |
| get_Enrichr | Source code |
| get_Enrichr_list | Source code |
| get_MEME_Output | Source code |
| get_Profile | Source code |
| get_limma | Source code |
| get_limma_tab | Source code |
| get_pattern_stats | Source code |
| get_tsne | Source code |
| ggheat | Source code |
| ggplotColors | Source code |
| ggplotScatter | Source code |
| gzfile | Source code |
| hh | Source code |
| ht | Source code |
| ks.default | Source code |
| last | Source code |
| letterA | Source code |
| letterC | Source code |
| letterG | Source code |
| letterT | Source code |
| list.bamfiles | Source code |
| list.bwfiles | Source code |
| list_star.logfiles | Source code |
| ln | Source code |
| lsos | Source code |
| makeBinaryContrasts | Source code |
| makeContlist | Source code |
| makePWM | Source code |
| many_kmeans | Source code |
| markExonNumber | Source code |
| multiplot | Source code |
| ncat | Source code |
| numlist | Source code |
| orderSeqnames | Source code |
| parseSalmonLog | Source code |
| parseSalmonStat | Source code |
| parse_BCFstats | Source code |
| parse_BCFstats_Files | Source code |
| parse_FastQC | Source code |
| parse_FastQCfile | Source code |
| parse_MEMEdb | Source code |
| parse_ScanGenome | Source code |
| parse_dreme | Source code |
| plot.clustergram | Source code |
| plotDESeqDiagnostics | Source code |
| plotExpression | Source code |
| plotLogo | Source code |
| plotMetaColumn | Source code |
| plotPCS | Source code |
| plot_Annotate_Bamfiles | Source code |
| plot_Enrichr | Source code |
| plot_MappingStats | Source code |
| plot_Profile | Source code |
| plot_TrimmingStats | Source code |
| plot_tsne | Source code |
| prepare_snRNA_Reads | Source code |
| pwm2cons | Source code |
| pwm2ic | Source code |
| readDECOD | Source code |
| readRDS_Integration | Source code |
| read_Annotation | Source code |
| read_ERCC | Source code |
| read_MEME | Source code |
| read_MEME_Output | Source code |
| read_SJ | Source code |
| read_rds_remote | Source code |
| read_rds_remote_file | Source code |
| read_xlsx_remote | Source code |
| reducer | Source code |
| regionError | Source code |
| resizeReads | Source code |
| runDECOD | Source code |
| run_BBduk2 | Source code |
| run_MAST | Source code |
| run_MEME | Source code |
| run_Paraclu | Source code |
| run_SmoothTest | Source code |
| run_Swembl | Source code |
| run_Trimming_BBduk2 | Source code |
| run_deepbind | Source code |
| run_dreme | Source code |
| run_kmerTSNE | Source code |
| run_scVI | Source code |
| run_tomtom | Source code Source code |
| sample_kmers | Source code |
| scan_Genome | Source code |
| select_Enrichr | Source code |
| select_Profile | Source code |
| smoothKmers | Source code |
| smoothKmersTime | Source code |
| smoothKmers_plot | Source code |
| source.lib | Source code |
| source.pro | Source code |
| split.numlist | Source code |
| stats_Salmon | Source code |
| summarize_tomtom | Source code |
| test_Enrichr | Source code |
| test_Swembl | Source code |
| writePWM | Source code Source code |
