Files in sagrudd/nanopoRe
Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/.gitignore
R/AlignmentPlots.R
R/BamParser.R
R/Checksums.R
R/EnrichmentPresentation.R
R/Environment.R
R/FileHandling.R
R/FlowcellLayout.R
R/InfographicPlot.R
R/JupyterRpy2.R
R/ONT_tutorial_sv.R
R/Phred.R
R/PlotsDepthOfCoverage.R
R/R_Results.R
R/RcppExports.R
R/ReferenceGenome.R
R/RepeatMasker.R
R/SequenceCharacteristics.R
R/SequencingSummary.R
R/SequencingSummaryBarcodes.R
R/SnifflesSV.R
R/TargetEnrichment.R
R/cigar.R
R/fast5.R
R/git.R
R/nanopore.R
R/sysdata.rda
R/tokens.R
R/zzz.R
README.md
inst/extdata/Ecoli_zymo_R10.fastq.gz
inst/extdata/Ecoli_zymo_R10_filt_subs.bam
inst/extdata/Ecoli_zymo_R10_filt_subs.bam.bai
inst/extdata/Escherichia_coli_complete_genome.fasta
inst/extdata/Escherichia_coli_complete_genome.fasta.fai
inst/extdata/GM24385.nf7.chr20.vcf
inst/extdata/ONT_logo.png
inst/extdata/barcoding_summary.txt.bz2
inst/extdata/cas9_FAK76554.bam
inst/extdata/cas9_FAK76554.bam.bai
inst/extdata/cas9_FAK76554.unmapped.quals
inst/extdata/cas9_FAK76554.unmapped.rcounts.Rdata
inst/extdata/cas9_FAK76554_aggregated_coverage.Rdata
inst/extdata/cas9_FAK76554_aggregated_offt_coverage.Rdata
inst/extdata/cas9_FAK76554_mapping_results.Rdata
inst/extdata/cas9_demo.yaml
inst/extdata/cas9_demo_ref.fasta
inst/extdata/cas9_demo_target.bed
inst/extdata/example.fastq.gz
inst/extdata/frankenFastq.fastq.gz
inst/extdata/sequencing_summary.txt.bz2
man/LeftRightPlot.Rd
man/RepeatMaskerGR.Rd
man/RunEnrichmentAnalysis.Rd
man/SVMappingCharacteristicTable.Rd
man/SequenceSummaryBarcodeHistogram.Rd
man/SequenceSummaryBarcodeInfoGraphic.Rd
man/SequenceSummaryBarcodeTable.Rd
man/SequenceSummaryBasicInfoPlot.Rd
man/SequenceSummaryExecutiveSummary.Rd
man/SequencingSummaryActiveChannelPlot.Rd
man/SequencingSummaryBarcodeMerge.Rd
man/SequencingSummaryBase50.Rd
man/SequencingSummaryChannelActivity.Rd
man/SequencingSummaryCumulativeBases.Rd
man/SequencingSummaryCumulativeReads.Rd
man/SequencingSummaryExtractRuntime.Rd
man/SequencingSummaryFlowCellID.Rd
man/SequencingSummaryGetPlatform.Rd
man/SequencingSummaryHasBarcodeInfo.Rd
man/SequencingSummaryPassGauge.Rd
man/SequencingSummaryReadLengthHistogram.Rd
man/SequencingSummaryReadLengthQualityDensity.Rd
man/SequencingSummaryReadQualityHistogram.Rd
man/SequencingSummarySpeedPlot.Rd
man/SequencingSummaryT50.Rd
man/SequencingSummaryTemporalThroughput.Rd
man/SequencingSummaryWeightedReadLength.Rd
man/Vcf2FilteredGranges.Rd
man/Vcf2GRanges.Rd
man/addCachedYAMLValue.Rd
man/bamSummarise.Rd
man/bamSummariseByChr.Rd
man/bamSummaryToCoverage.Rd
man/buildPositionMap.Rd
man/cachedYAMLToYAML.Rd
man/chromosomeMappingSummary.Rd
man/cigarQ2Op.Rd
man/cigarQ2R.Rd
man/cigarR2Op.Rd
man/cigarR2Q.Rd
man/cleanReferenceGenome.Rd
man/enrichmentCoverageTypeOverChromosomes.Rd
man/enrichmentExecutiveSummary.Rd
man/enrichmentGetTargetList.Rd
man/enrichmentMappingByGenomicSegment.Rd
man/enrichmentMultiGeneCoveragePanel.Rd
man/enrichmentOffTargetKaryogram.Rd
man/enrichmentOffTargetTable.Rd
man/enrichmentSingleTargetPlot.Rd
man/enrichmentStrandedTargetPlot.Rd
man/enrichmentTargetPerformanceTable.Rd
man/enrichmentWriteExcelOffTarget.Rd
man/enrichmentWriteExcelOnTarget.Rd
man/extract5mC.Rd
man/extract5mCProbabilities.Rd
man/extractMethylatedBases.Rd
man/fastqCheckup.Rd
man/fastqValidator.Rd
man/fixFastq.Rd
man/getCachedYAMLFields.Rd
man/getCachedYAMLValue.Rd
man/getChromosomeIds.Rd
man/getChromosomeSequence.Rd
man/getFastqBases.Rd
man/getFastqCount.Rd
man/getFastqPlusErrorCount.Rd
man/getFlongleChannelMap.Rd
man/getGitDescription.Rd
man/getMalformedFastqHeaderCount.Rd
man/getMinIONChannelMap.Rd
man/getOutputFormat.Rd
man/getPlotDimensions.Rd
man/getPromethIONChannelMap.Rd
man/getReferenceGenome.Rd
man/getReferenceGenomeGR.Rd
man/getRpath.Rd
man/getSeqLengths.Rd
man/getSequenceQualityMismatchCount.Rd
man/getSkippedLineCount.Rd
man/getStringSetId.Rd
man/getZeroLengthSequenceCount.Rd
man/ggbiosave.Rd
man/hasCachedYAMLField.Rd
man/importConfigYAML.Rd
man/importEnrichmentResults.Rd
man/importSequencingSummary.Rd
man/infoGraphicPlot3.Rd
man/infoGraphicPlot4.Rd
man/infoGraphicPlot5.Rd
man/init.Rd
man/isEnrichmentAnalysisComplete.Rd
man/isInitialised.Rd
man/lcalc.Rd
man/listCachedObjects.Rd
man/listOutputFormat.Rd
man/loadMethylationBamFile.Rd
man/loadReferenceGenome.Rd
man/md5sum.Rd
man/nanopoRe.Rd
man/ncalc.Rd
man/parallelBamSummarise.Rd
man/phredmean.Rd
man/plotAlignmentAccuracy.Rd
man/plotAlignmentIdentity.Rd
man/plotDepthOfCoverageMegablock.Rd
man/plotOverallCovHistogram.Rd
man/qualToMeanQ.Rd
man/setCachedYAMLValue.Rd
man/setLogFile.Rd
man/setOutputFormat.Rd
man/setPlotDimensions.Rd
man/setReferenceGenome.Rd
man/setRpath.Rd
man/snifflesKaryogram.Rd
man/svLengthDistribution.Rd
man/testBam.Rd
man/unsetLog.Rd
nanopoRe.Rproj
src/.gitignore
src/Makevars
src/RcppExports.cpp
src/fastqValidator.cpp
tests/testthat.R
tests/testthat/test_bam.R
tests/testthat/test_cas9.R
tests/testthat/test_invalidfastqfile.R
tests/testthat/test_md5sum.R
tests/testthat/test_reference_genomes.R
tests/testthat/test_sequencesummary.R
tests/testthat/test_validfastqfile.R
vignettes/bam_analysis.Rmd
vignettes/cas9.Rmd
vignettes/flowcell_layout.Rmd
vignettes/nanopoRe.Rmd
vignettes/sequencing_summary.Rmd
vignettes/sequencing_summary_pion_report.Rmd
