Files in AngelCampos/tx_tools
An R package facilitating analysis of RNA modifications, structures, and interactions

.Rbuildignore
.Rprofile
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md R/alias.R R/data.R R/deprecated.R R/experimental.R R/helpers.R R/tx_core.R R/tx_plots.R R/ver_notes.R README.Rmd README.md WIP.R
_pkgdown.yml
data-raw/dataRecipe-R.R
data/IUPAC_CODE_MAP_extended.rda
data/IUPAC_code_2nucs.rda
data/IUPAC_code_simpl.rda
data/annotSites_RRACH.rda
data/bam_sk1.rda
data/gA_sk1.rda
data/genome_sk1.rda
data/sc_rRNAmods_Taoka.rda
data/sc_txDTL.rda
data/txCoreCols.rda
data/txCoreCols_refSeq.rda
data/txDTL_Tk.rda
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
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docs/apple-touch-icon-152x152.png
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docs/articles/index.html
docs/articles/txtools.html
docs/articles/txtools_files/figure-html/unnamed-chunk-18-1.png
docs/articles/txtools_files/figure-html/unnamed-chunk-19-1.png
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docs/authors.html
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.2.2/bootstrap.min.css
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/IUPAC_CODE_MAP_extended.html
docs/reference/IUPAC_code_2nucs.html
docs/reference/IUPAC_code_simpl.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/annotSites_RRACH.html
docs/reference/bam_sk1.html
docs/reference/figures/README-plotNucFreq-1.png
docs/reference/figures/lifecycle-archived.svg
docs/reference/figures/lifecycle-defunct.svg
docs/reference/figures/lifecycle-deprecated.svg
docs/reference/figures/lifecycle-experimental.svg
docs/reference/figures/lifecycle-maturing.svg
docs/reference/figures/lifecycle-questioning.svg
docs/reference/figures/lifecycle-stable.svg
docs/reference/figures/lifecycle-superseded.svg
docs/reference/figures/logo.png
docs/reference/figures/readme_1.png
docs/reference/figures/readme_2.png
docs/reference/gA_sk1.html
docs/reference/genome_sk1.html
docs/reference/getDumpedAlignments.html
docs/reference/hid_aggregate_DTlist.html
docs/reference/hlp_coverageTab_mc.html
docs/reference/hlp_genCoorTab_mc.html
docs/reference/hlp_nucFreqTab_mc.html
docs/reference/hlp_plot_metageneRegions.html
docs/reference/index.html
docs/reference/mm_geneAnnot.html
docs/reference/sc_faGenome.html
docs/reference/sc_geneAnnot.html
docs/reference/sc_rRNAmods_Taoka.html
docs/reference/sc_txDTL.html
docs/reference/tk_faGenome.html
docs/reference/tk_geneAnnot.html
docs/reference/txCoreCols.html
docs/reference/txCoreCols_refSeq.html
docs/reference/txDTL_Tk.html
docs/reference/tx_add_diffNucToRef.html
docs/reference/tx_add_diffNucToRefRatio.html
docs/reference/tx_add_endRatio.html
docs/reference/tx_add_endRatio1bpDS.html
docs/reference/tx_add_endRatio1bpUS.html
docs/reference/tx_add_exonNumber.html
docs/reference/tx_add_exonPlace.html
docs/reference/tx_add_geneRegion.html
docs/reference/tx_add_misincCount.html
docs/reference/tx_add_misincRate.html
docs/reference/tx_add_misincRateNucSpec.html
docs/reference/tx_add_motifPresence.html
docs/reference/tx_add_nucTotal.html
docs/reference/tx_add_pos.html
docs/reference/tx_add_refSeqDT.html
docs/reference/tx_add_relTxPos.html
docs/reference/tx_add_rollingMean.html
docs/reference/tx_add_siteAnnotation.html
docs/reference/tx_add_spliceSitesLogical.html
docs/reference/tx_add_startRatio.html
docs/reference/tx_add_startRatio1bpDS.html
docs/reference/tx_add_startRatio1bpUS.html
docs/reference/tx_combineTxReads.html
docs/reference/tx_complete_DT.html
docs/reference/tx_counts.html
docs/reference/tx_cutEnds_DT.html
docs/reference/tx_cut_geneAnnotBytxDT.html
docs/reference/tx_data_caseStudy2.html
docs/reference/tx_dm3_geneAnnot.html
docs/reference/tx_extend_UTR.html
docs/reference/tx_filter_maxWidth.html
docs/reference/tx_generatePairedEndFASTQ.html
docs/reference/tx_generateSingleEndFASTQ.html
docs/reference/tx_get_flankSequence.html
docs/reference/tx_get_flanksFromLogicAnnot.html
docs/reference/tx_get_geneLengths.html
docs/reference/tx_get_metageneAtCDS.html
docs/reference/tx_get_metageneExons.html
docs/reference/tx_get_metageneRegions.html
docs/reference/tx_get_transcriptSeqs.html
docs/reference/tx_get_unassignedAlignments.html
docs/reference/tx_load_bam.html
docs/reference/tx_load_bed.html
docs/reference/tx_load_genome.html
docs/reference/tx_load_rdsDT.html
docs/reference/tx_makeDT_covNucFreq.html
docs/reference/tx_makeDT_coverage.html
docs/reference/tx_makeDT_nucFreq.html
docs/reference/tx_merge_DT.html
docs/reference/tx_orderDT.html
docs/reference/tx_plot_ggseqlogo.html
docs/reference/tx_plot_metaGeneByBins.html
docs/reference/tx_plot_metageneAtCDS.html
docs/reference/tx_plot_metageneExons.html
docs/reference/tx_plot_metageneRegions.html
docs/reference/tx_plot_nucFreq.html
docs/reference/tx_plot_numeric-1.png
docs/reference/tx_plot_numeric-2.png
docs/reference/tx_plot_numeric.html
docs/reference/tx_plot_staEndCov.html
docs/reference/tx_reads.html
docs/reference/tx_sampleByGenes.html
docs/reference/tx_sample_GRList.html
docs/reference/tx_shift_geneWise.html
docs/reference/tx_split_DT.html
docs/reference/tx_test_LRTedgeR.html
docs/reference/tx_test_ttest.html
docs/reference/tx_unifyTxDTL.html
docs/reference/txtools.html
docs/reference/window_around.html
docs/search.json
docs/sitemap.xml
inst/CITATION
inst/bam2txDT.R
inst/extdata/example_hg19.bam
inst/extdata/toyGeneAnnot_Dmelan_chr4.bed
inst/extdata/twoUCSCgenes_hg19.bed
man/IUPAC_CODE_MAP_extended.Rd man/IUPAC_code_2nucs.Rd man/IUPAC_code_simpl.Rd man/annotSites_RRACH.Rd man/bam_sk1.Rd
man/figures/README-plotNucFreq-1.png
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/figures/logo.png
man/figures/readme_1.png
man/figures/readme_2.png
man/gA_sk1.Rd man/genome_sk1.Rd man/getDumpedAlignments.Rd man/hid_aggregate_DTlist.Rd man/hlp_coverageTab_mc.Rd man/hlp_genCoorTab_mc.Rd man/hlp_nucFreqTab_mc.Rd man/hlp_plot_metageneRegions.Rd man/mm_geneAnnot.Rd man/sc_faGenome.Rd man/sc_geneAnnot.Rd man/sc_rRNAmods_Taoka.Rd man/sc_txDTL.Rd man/tk_faGenome.Rd man/tk_geneAnnot.Rd man/txCoreCols.Rd man/txCoreCols_refSeq.Rd man/txDTL_Tk.Rd man/tx_add_diffNucToRef.Rd man/tx_add_diffNucToRefRatio.Rd man/tx_add_endRatio.Rd man/tx_add_endRatio1bpDS.Rd man/tx_add_endRatio1bpUS.Rd man/tx_add_exonNumber.Rd man/tx_add_exonPlace.Rd man/tx_add_geneRegion.Rd man/tx_add_misincCount.Rd man/tx_add_misincRate.Rd man/tx_add_misincRateNucSpec.Rd man/tx_add_motifPresence.Rd man/tx_add_nucTotal.Rd man/tx_add_pos.Rd man/tx_add_refSeqDT.Rd man/tx_add_relTxPos.Rd man/tx_add_rollingMean.Rd man/tx_add_siteAnnotation.Rd man/tx_add_spliceSitesLogical.Rd man/tx_add_startRatio.Rd man/tx_add_startRatio1bpDS.Rd man/tx_add_startRatio1bpUS.Rd man/tx_combineTxReads.Rd man/tx_complete_DT.Rd man/tx_counts.Rd man/tx_cutEnds_DT.Rd man/tx_cut_geneAnnotBytxDT.Rd man/tx_data_caseStudy2.Rd man/tx_dm3_geneAnnot.Rd man/tx_extend_UTR.Rd man/tx_filter_maxWidth.Rd man/tx_generatePairedEndFASTQ.Rd man/tx_generateSingleEndFASTQ.Rd man/tx_get_flankSequence.Rd man/tx_get_flanksFromLogicAnnot.Rd man/tx_get_geneLengths.Rd man/tx_get_metageneAtCDS.Rd man/tx_get_metageneExons.Rd man/tx_get_metageneRegions.Rd man/tx_get_transcriptSeqs.Rd man/tx_get_unassignedAlignments.Rd man/tx_load_bam.Rd man/tx_load_bed.Rd man/tx_load_genome.Rd man/tx_load_rdsDT.Rd man/tx_makeDT_covNucFreq.Rd man/tx_makeDT_coverage.Rd man/tx_makeDT_nucFreq.Rd man/tx_merge_DT.Rd man/tx_orderDT.Rd man/tx_plot_ggseqlogo.Rd man/tx_plot_metaGeneByBins.Rd man/tx_plot_metageneAtCDS.Rd man/tx_plot_metageneExons.Rd man/tx_plot_metageneRegions.Rd man/tx_plot_nucFreq.Rd man/tx_plot_numeric.Rd man/tx_plot_staEndCov.Rd man/tx_reads.Rd man/tx_sampleByGenes.Rd man/tx_sample_GRList.Rd man/tx_shift_geneWise.Rd man/tx_split_DT.Rd man/tx_test_LRTedgeR.Rd man/tx_test_ttest.Rd man/tx_unifyTxDTL.Rd man/txtools.Rd man/window_around.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
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pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
references.bib
tests/testthat.R tests/testthat/test-txtools.R
txtools.Rproj
vignettes/.gitignore
vignettes/txtools.Rmd
AngelCampos/tx_tools documentation built on Sept. 17, 2024, 1:27 a.m.