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

.Rbuildignore

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DESCRIPTION

LICENSE

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/reference/IUPAC_CODE_MAP_extended.html

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docs/reference/gA_sk1.html

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docs/reference/getDumpedAlignments.html

docs/reference/hid_aggregate_DTlist.html

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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

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docs/reference/tx_combineTxReads.html

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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

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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

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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.

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

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

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

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

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

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