├── .Rbuildignore ├── .Rprofile ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── alias.R ├── data.R ├── deprecated.R ├── experimental.R ├── helpers.R ├── tx_core.R ├── tx_plots.R └── ver_notes.R ├── README.Rmd ├── README.md ├── WIP.R ├── _pkgdown.yml ├── data-raw └── dataRecipe-R.R ├── data ├── IUPAC_CODE_MAP_extended.rda ├── IUPAC_code_2nucs.rda ├── IUPAC_code_simpl.rda ├── annotSites_RRACH.rda ├── bam_sk1.rda ├── gA_sk1.rda ├── genome_sk1.rda ├── sc_rRNAmods_Taoka.rda ├── sc_txDTL.rda ├── txCoreCols.rda ├── txCoreCols_refSeq.rda └── txDTL_Tk.rda ├── docs ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── index.html │ ├── txtools.html │ └── txtools_files │ │ └── figure-html │ │ ├── unnamed-chunk-18-1.png │ │ ├── unnamed-chunk-19-1.png │ │ ├── unnamed-chunk-21-1.png │ │ ├── unnamed-chunk-22-1.png │ │ ├── unnamed-chunk-23-1.png │ │ ├── unnamed-chunk-23-2.png │ │ ├── unnamed-chunk-24-1.png │ │ └── unnamed-chunk-25-1.png ├── authors.html ├── deps │ ├── bootstrap-5.2.2 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── data-deps.txt │ └── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── link.svg ├── logo.png ├── news │ └── index.html ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── IUPAC_CODE_MAP_extended.html │ ├── IUPAC_code_2nucs.html │ ├── IUPAC_code_simpl.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── annotSites_RRACH.html │ ├── bam_sk1.html │ ├── figures │ │ ├── README-plotNucFreq-1.png │ │ ├── lifecycle-archived.svg │ │ ├── lifecycle-defunct.svg │ │ ├── lifecycle-deprecated.svg │ │ ├── lifecycle-experimental.svg │ │ ├── lifecycle-maturing.svg │ │ ├── lifecycle-questioning.svg │ │ ├── lifecycle-stable.svg │ │ ├── lifecycle-superseded.svg │ │ ├── logo.png │ │ ├── readme_1.png │ │ └── readme_2.png │ ├── gA_sk1.html │ ├── genome_sk1.html │ ├── getDumpedAlignments.html │ ├── hid_aggregate_DTlist.html │ ├── hlp_coverageTab_mc.html │ ├── hlp_genCoorTab_mc.html │ ├── hlp_nucFreqTab_mc.html │ ├── hlp_plot_metageneRegions.html │ ├── index.html │ ├── mm_geneAnnot.html │ ├── sc_faGenome.html │ ├── sc_geneAnnot.html │ ├── sc_rRNAmods_Taoka.html │ ├── sc_txDTL.html │ ├── tk_faGenome.html │ ├── tk_geneAnnot.html │ ├── txCoreCols.html │ ├── txCoreCols_refSeq.html │ ├── txDTL_Tk.html │ ├── tx_add_diffNucToRef.html │ ├── tx_add_diffNucToRefRatio.html │ ├── tx_add_endRatio.html │ ├── tx_add_endRatio1bpDS.html │ ├── tx_add_endRatio1bpUS.html │ ├── tx_add_exonNumber.html │ ├── tx_add_exonPlace.html │ ├── tx_add_geneRegion.html │ ├── tx_add_misincCount.html │ ├── tx_add_misincRate.html │ ├── tx_add_misincRateNucSpec.html │ ├── tx_add_motifPresence.html │ ├── tx_add_nucTotal.html │ ├── tx_add_pos.html │ ├── tx_add_refSeqDT.html │ ├── tx_add_relTxPos.html │ ├── tx_add_rollingMean.html │ ├── tx_add_siteAnnotation.html │ ├── tx_add_spliceSitesLogical.html │ ├── tx_add_startRatio.html │ ├── tx_add_startRatio1bpDS.html │ ├── tx_add_startRatio1bpUS.html │ ├── tx_combineTxReads.html │ ├── tx_complete_DT.html │ ├── tx_counts.html │ ├── tx_cutEnds_DT.html │ ├── tx_cut_geneAnnotBytxDT.html │ ├── tx_data_caseStudy2.html │ ├── tx_dm3_geneAnnot.html │ ├── tx_extend_UTR.html │ ├── tx_filter_maxWidth.html │ ├── tx_generatePairedEndFASTQ.html │ ├── tx_generateSingleEndFASTQ.html │ ├── tx_get_flankSequence.html │ ├── tx_get_flanksFromLogicAnnot.html │ ├── tx_get_geneLengths.html │ ├── tx_get_metageneAtCDS.html │ ├── tx_get_metageneExons.html │ ├── tx_get_metageneRegions.html │ ├── tx_get_transcriptSeqs.html │ ├── tx_get_unassignedAlignments.html │ ├── tx_load_bam.html │ ├── tx_load_bed.html │ ├── tx_load_genome.html │ ├── tx_load_rdsDT.html │ ├── tx_makeDT_covNucFreq.html │ ├── tx_makeDT_coverage.html │ ├── tx_makeDT_nucFreq.html │ ├── tx_merge_DT.html │ ├── tx_orderDT.html │ ├── tx_plot_ggseqlogo.html │ ├── tx_plot_metaGeneByBins.html │ ├── tx_plot_metageneAtCDS.html │ ├── tx_plot_metageneExons.html │ ├── tx_plot_metageneRegions.html │ ├── tx_plot_nucFreq.html │ ├── tx_plot_numeric-1.png │ ├── tx_plot_numeric-2.png │ ├── tx_plot_numeric.html │ ├── tx_plot_staEndCov.html │ ├── tx_reads.html │ ├── tx_sampleByGenes.html │ ├── tx_sample_GRList.html │ ├── tx_shift_geneWise.html │ ├── tx_split_DT.html │ ├── tx_test_LRTedgeR.html │ ├── tx_test_ttest.html │ ├── tx_unifyTxDTL.html │ ├── txtools.html │ └── window_around.html ├── search.json └── sitemap.xml ├── inst ├── CITATION ├── bam2txDT.R └── extdata │ ├── example_hg19.bam │ ├── toyGeneAnnot_Dmelan_chr4.bed │ └── twoUCSCgenes_hg19.bed ├── man ├── IUPAC_CODE_MAP_extended.Rd ├── IUPAC_code_2nucs.Rd ├── IUPAC_code_simpl.Rd ├── annotSites_RRACH.Rd ├── bam_sk1.Rd ├── figures │ ├── README-plotNucFreq-1.svg │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ ├── logo.png │ ├── readme_1.png │ └── readme_2.png ├── gA_sk1.Rd ├── genome_sk1.Rd ├── getDumpedAlignments.Rd ├── hid_aggregate_DTlist.Rd ├── hlp_coverageTab_mc.Rd ├── hlp_genCoorTab_mc.Rd ├── hlp_nucFreqTab_mc.Rd ├── hlp_plot_metageneRegions.Rd ├── mm_geneAnnot.Rd ├── sc_faGenome.Rd ├── sc_geneAnnot.Rd ├── sc_rRNAmods_Taoka.Rd ├── sc_txDTL.Rd ├── tk_faGenome.Rd ├── tk_geneAnnot.Rd ├── txCoreCols.Rd ├── txCoreCols_refSeq.Rd ├── txDTL_Tk.Rd ├── tx_add_diffNucToRef.Rd ├── tx_add_diffNucToRefRatio.Rd ├── tx_add_endRatio.Rd ├── tx_add_endRatio1bpDS.Rd ├── tx_add_endRatio1bpUS.Rd ├── tx_add_exonNumber.Rd ├── tx_add_exonPlace.Rd ├── tx_add_geneRegion.Rd ├── tx_add_misincCount.Rd ├── tx_add_misincRate.Rd ├── tx_add_misincRateNucSpec.Rd ├── tx_add_motifPresence.Rd ├── tx_add_nucTotal.Rd ├── tx_add_pos.Rd ├── tx_add_refSeqDT.Rd ├── tx_add_relTxPos.Rd ├── tx_add_rollingMean.Rd ├── tx_add_siteAnnotation.Rd ├── tx_add_spliceSitesLogical.Rd ├── tx_add_startRatio.Rd ├── tx_add_startRatio1bpDS.Rd ├── tx_add_startRatio1bpUS.Rd ├── tx_combineTxReads.Rd ├── tx_complete_DT.Rd ├── tx_counts.Rd ├── tx_cutEnds_DT.Rd ├── tx_cut_geneAnnotBytxDT.Rd ├── tx_data_caseStudy2.Rd ├── tx_dm3_geneAnnot.Rd ├── tx_extend_UTR.Rd ├── tx_filter_maxWidth.Rd ├── tx_generatePairedEndFASTQ.Rd ├── tx_generateSingleEndFASTQ.Rd ├── tx_get_flankSequence.Rd ├── tx_get_flanksFromLogicAnnot.Rd ├── tx_get_geneLengths.Rd ├── tx_get_metageneAtCDS.Rd ├── tx_get_metageneExons.Rd ├── tx_get_metageneRegions.Rd ├── tx_get_transcriptSeqs.Rd ├── tx_get_unassignedAlignments.Rd ├── tx_load_bam.Rd ├── tx_load_bed.Rd ├── tx_load_genome.Rd ├── tx_load_rdsDT.Rd ├── tx_makeDT_covNucFreq.Rd ├── tx_makeDT_coverage.Rd ├── tx_makeDT_nucFreq.Rd ├── tx_merge_DT.Rd ├── tx_orderDT.Rd ├── tx_plot_ggseqlogo.Rd ├── tx_plot_metaGeneByBins.Rd ├── tx_plot_metageneAtCDS.Rd ├── tx_plot_metageneExons.Rd ├── tx_plot_metageneRegions.Rd ├── tx_plot_nucFreq.Rd ├── tx_plot_numeric.Rd ├── tx_plot_staEndCov.Rd ├── tx_reads.Rd ├── tx_sampleByGenes.Rd ├── tx_sample_GRList.Rd ├── tx_shift_geneWise.Rd ├── tx_split_DT.Rd ├── tx_test_LRTedgeR.Rd ├── tx_test_ttest.Rd ├── tx_unifyTxDTL.Rd ├── txtools.Rd └── window_around.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── references.bib ├── tests ├── testthat.R └── testthat │ └── test-txtools.R ├── txtools.Rproj └── vignettes ├── .gitignore └── txtools.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- 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