API for AngelCampos/tx_tools
An R package facilitating analysis of RNA modifications, structures, and interactions
| Global functions | |
|---|---|
| .dumpEnvirTxtools | Source code |
| IUPAC_CODE_MAP_extended | Man page |
| IUPAC_code_2nucs | Man page |
| IUPAC_code_simpl | Man page |
| annotSites_RRACH | Man page |
| bam_sk1 | Man page |
| check_BAM_has_seq | Source code |
| check_DFforGRanges | Source code |
| check_DT | Source code |
| check_DThasCol | Source code |
| check_GA_genome_chrCompat | Source code |
| check_GA_reads_compatibility | Source code |
| check_GA_txDT_compat | Source code |
| check_GR_has_seq | Source code |
| check_funsPkg | Source code |
| check_integerGreaterThanZero_arg | Source code |
| check_integer_arg | Source code |
| check_mc_windows | Source code |
| check_refSeq | Source code |
| check_sameGenesInDTL | Source code |
| check_windows | Source code |
| exonBlockGen | Source code |
| exonGRanges | Source code |
| gA_sk1 | Man page |
| genome_sk1 | Man page |
| getDumpedAlignments | Man page Source code |
| hid_aggregate_DTlist | Man page |
| hlp_addMissingNucs | Source code |
| hlp_add_motifPresence | Source code |
| hlp_cbind2Tabs | Source code |
| hlp_cbind3Tabs | Source code |
| hlp_cleanBam_emptySeq | Source code |
| hlp_coverage | Source code |
| hlp_coverageTab | Source code |
| hlp_coverageTab_mc | Man page Source code |
| hlp_dump_notAssigned | Source code |
| hlp_genCoorTab_mc | Man page Source code |
| hlp_getVectorElements | Source code |
| hlp_nucFreqTab_mc | Man page Source code |
| hlp_plot_metageneRegions | Man page |
| hlp_removeColumnIfPresent | Source code |
| hlp_remove_UTR | Source code |
| hlp_splLog | Source code |
| hlp_splitNucsForceInt | Source code |
| hlp_splitNucsHalf | Source code |
| hlpr_ReadsInGene | Source code |
| hlpr_ReadsInGene_SingleEnd | Source code |
| hlpr_genCoorTabGenes | Source code |
| hlpr_splitReadsByGenes | Source code |
| hlpr_splitReadsByGenes_singleEnd | Source code |
| if_IRangesList_Unlist | Source code |
| indexAlignmentsByGenomicRegion | Source code |
| mm_geneAnnot | Man page Source code |
| oSize | Source code |
| oppStrand | Source code |
| rmAmbigStrandAligns | Source code |
| rowMeansColG | Source code |
| sc_faGenome | Man page Source code |
| sc_geneAnnot | Man page Source code |
| sc_rRNAmods_Taoka | Man page |
| sc_txDTL | Man page |
| scale_fill_txBrowser | Source code |
| scale_fill_txBrowser_2 | Source code |
| stretchBlocks_3p | Source code |
| stretchBlocks_5p | Source code |
| tk_faGenome | Man page Source code |
| tk_geneAnnot | Man page Source code |
| txBrowser_pal | Source code |
| txBrowser_pal_2 | Source code |
| txCoreCols | Man page |
| txCoreCols_refSeq | Man page |
| txDTL_Tk | Man page |
| tx_add_diffNucToRef | Man page Source code |
| tx_add_diffNucToRefRatio | Man page Source code |
| tx_add_endRatio | Man page Source code |
| tx_add_endRatio1bpDS | Man page Source code |
| tx_add_endRatio1bpUS | Man page Source code |
| tx_add_exonNumber | Man page Source code |
| tx_add_exonPlace | Man page Source code |
| tx_add_geneRegion | Man page Source code |
| tx_add_misincCount | Man page Source code |
| tx_add_misincRate | Man page Source code |
| tx_add_misincRateNucSpec | Man page Source code |
| tx_add_misincorpRateNucSpec | Man page Source code |
| tx_add_motifPresence | Man page |
| tx_add_nucTotal | Man page Source code |
| tx_add_pos | Man page Source code |
| tx_add_refSeqDT | Man page Source code |
| tx_add_relTxPos | Man page Source code |
| tx_add_rollingMean | Man page Source code |
| tx_add_siteAnnotation | Man page |
| tx_add_spliceSitesLogical | Man page Source code |
| tx_add_startRatio | Man page Source code |
| tx_add_startRatio1bpDS | Man page Source code |
| tx_add_startRatio1bpUS | Man page Source code |
| tx_combineTxReads | Man page Source code |
| tx_complete_DT | Man page Source code |
| tx_counts | Man page Source code |
| tx_covNucFreqDT | Man page Source code |
| tx_coverageDT | Man page Source code |
| tx_cutEnds_DT | Man page Source code |
| tx_cut_geneAnnotBytxDT | Man page Source code |
| tx_data_caseStudy2 | Man page Source code |
| tx_dm3_geneAnnot | Man page Source code |
| tx_extend_UTR | Man page Source code |
| tx_filter_maxWidth | Man page Source code |
| tx_filter_max_width | Man page Source code |
| tx_flushUnassigned | Man page Source code |
| tx_generatePairedEndFASTQ | Man page Source code |
| tx_generateSingleEndFASTQ | Man page Source code |
| tx_getUnassignedAlignments | Man page Source code |
| tx_get_flankSequence | Man page Source code |
| tx_get_flanksFromLogicAnnot | Man page Source code |
| tx_get_geneLengths | Man page Source code |
| tx_get_metageneAtCDS | Man page Source code |
| tx_get_metageneExons | Man page Source code |
| tx_get_metageneRegions | Man page Source code |
| tx_get_transcriptSeqs | Man page Source code |
| tx_get_unassignedAlignments | Man page Source code |
| tx_load_bam | Man page Source code |
| tx_load_bed | Man page Source code |
| tx_load_genome | Man page Source code |
| tx_load_rdsDT | Man page Source code |
| tx_makeDT_covNucFreq | Man page Source code |
| tx_makeDT_coverage | Man page Source code |
| tx_makeDT_nucFreq | Man page Source code |
| tx_merge_DT | Man page Source code |
| tx_nucFreqDT | Man page Source code |
| tx_orderDT | Man page Source code |
| tx_plot_ggseqlogo | Man page Source code |
| tx_plot_metaGeneByBins | Man page Source code |
| tx_plot_metageneAtCDS | Man page Source code |
| tx_plot_metageneExons | Man page Source code |
| tx_plot_metageneRegions | Man page Source code |
| tx_plot_nucFreq | Man page Source code |
| tx_plot_numeric | Man page Source code |
| tx_plot_staEndCov | Man page Source code |
| tx_reads | Man page Source code |
| tx_reads_mc | Man page Source code |
| tx_sampleByGenes | Man page Source code |
| tx_sample_GRList | Man page Source code |
| tx_shift_geneWise | Man page Source code |
| tx_split_DT | Man page Source code |
| tx_test_LRTedgeR | Man page Source code |
| tx_test_ttest | Man page Source code |
| tx_unifyTxDTL | Man page Source code |
| txtools | Man page |
| txtools-package | Man page |
| warn_nCores | Source code |
| window_around | Man page Source code |
