Files in valenlab/amplican

Automated analysis of CRISPR experiments

R/AlignmentsExperimentSet-class.R R/RcppExports.R R/amplican.R R/amplicanAlign.R R/amplicanFilter.R R/amplicanNormalize.R R/amplicanReport.R R/amplicanSummarize.R R/ggforce_bezier.R R/helpers_alignment.R R/helpers_directory.R R/helpers_filters.R R/helpers_general.R R/helpers_plots.R R/helpers_rmd.R R/helpers_warnings.R README.md inst/rmarkdown/templates/amplicon_report/skeleton/skeleton.Rmd inst/rmarkdown/templates/barcode_report/skeleton/skeleton.Rmd inst/rmarkdown/templates/group_report/skeleton/skeleton.Rmd inst/rmarkdown/templates/guide_report/skeleton/skeleton.Rmd inst/rmarkdown/templates/id_report/skeleton/skeleton.Rmd inst/rmarkdown/templates/index_report/skeleton/skeleton.Rmd man/AlignmentsExperimentSet-class.Rd man/alphabetQuality.Rd man/amplican.Rd man/amplicanAlign.Rd man/amplicanConsensus.Rd man/amplicanFilter.Rd man/amplicanMap.Rd man/amplicanNormalize.Rd man/amplicanOverlap.Rd man/amplicanPipeline.Rd man/amplicanPipelineConservative.Rd man/amplicanReport.Rd man/amplicanSummarize.Rd man/amplican_print_reads.Rd man/assignedCount.Rd man/barcodeData-set.Rd man/barcodeData.Rd man/checkConfigFile.Rd man/checkFileWriteAccess.Rd man/checkPrimers.Rd man/checkTarget.Rd man/cigarsToEvents.Rd man/comb_along.Rd man/cumsumw.Rd man/decode.Rd man/defGR.Rd man/experimentData-set.Rd man/experimentData.Rd man/extractEvents.Rd man/findEOP.Rd man/findLQR.Rd man/findPD.Rd man/flipRanges.Rd man/fwdReads-set.Rd man/fwdReads.Rd man/fwdReadsType-set.Rd man/fwdReadsType.Rd man/geom_bezier.Rd man/getEventInfo.Rd man/getEvents.Rd man/get_left_primer.Rd man/get_right_primer.Rd man/get_seq.Rd man/goodAvgQuality.Rd man/goodBaseQuality.Rd man/is_hdr_strict.Rd man/lookupAlignment.Rd man/makeAlignment.Rd man/metaplot_deletions.Rd man/metaplot_insertions.Rd man/metaplot_mismatches.Rd man/pairToEvents.Rd man/plot_amplicon.Rd man/plot_cuts.Rd man/plot_deletions.Rd man/plot_height.Rd man/plot_heterogeneity.Rd man/plot_insertions.Rd man/plot_mismatches.Rd man/plot_variants.Rd man/readCounts-set.Rd man/readCounts.Rd man/revComp.Rd man/rveReads-set.Rd man/rveReads.Rd man/rveReadsType-set.Rd man/rveReadsType.Rd man/unassignedCount.Rd man/unassignedData-set.Rd man/unassignedData.Rd man/upperGroups.Rd man/writeAlignments.Rd tests/testthat.R tests/testthat/Rplots.pdf tests/testthat/test_alignment_helpers.R tests/testthat/test_amplican.R tests/testthat/test_filters_helpers.R tests/testthat/test_general_helpers.R tests/testthat/test_plot_helpers.R tests/testthat/test_summary_helpers.R vignettes/amplicanFAQ.Rmd vignettes/amplicanOverview.Rmd vignettes/example_amplicon_report.Rmd vignettes/example_barcode_report.Rmd vignettes/example_group_report.Rmd vignettes/example_guide_report.Rmd vignettes/example_id_report.Rmd vignettes/example_index.Rmd