Files in amplican

Automated analysis of CRISPR experiments

README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

src/RcppExports.cpp

src/bezier.cpp

R/helpers_filters.R R/helpers_rmd.R R/amplicanAlign.R R/helpers_general.R R/amplicanNormalize.R R/AlignmentsExperimentSet-class.R R/helpers_alignment.R R/RcppExports.R R/helpers_warnings.R R/amplicanSummarize.R R/amplicanFilter.R R/helpers_directory.R R/ggforce_bezier.R R/amplicanReport.R R/helpers_plots.R R/amplican.R vignettes/example_id_report.Rmd vignettes/example_barcode_report.Rmd vignettes/example_group_report.Rmd vignettes/amplicanFAQ.Rmd vignettes/example_amplicon_report.Rmd vignettes/example_index.Rmd vignettes/amplicanOverview.Rmd vignettes/example_guide_report.Rmd

vignettes/figures/indel_rate_vs_indel_size.png

vignettes/figures/amplican_conceptual_map.png

vignettes/figures/amplican_consensus_rules.png

man/fwdReads.Rd man/upperGroups.Rd man/plot_amplicon.Rd man/plot_deletions.Rd man/amplicanOverlap.Rd man/getEventInfo.Rd man/assignedCount.Rd man/rveReads.Rd man/amplicanAlign.Rd man/barcodeData-set.Rd man/writeAlignments.Rd man/defGR.Rd man/AlignmentsExperimentSet-class.Rd man/amplicanNormalize.Rd man/findLQR.Rd man/checkTarget.Rd man/flipRanges.Rd man/goodBaseQuality.Rd man/experimentData-set.Rd man/plot_mismatches.Rd man/fwdReads-set.Rd man/amplicanConsensus.Rd man/decode.Rd man/experimentData.Rd man/readCounts.Rd man/amplicanPipeline.Rd man/plot_height.Rd man/goodAvgQuality.Rd man/checkFileWriteAccess.Rd man/plot_heterogeneity.Rd man/rveReads-set.Rd man/pairToEvents.Rd man/amplican.Rd man/amplicanSummarize.Rd man/fwdReadsType-set.Rd man/plot_variants.Rd man/amplicanMap.Rd man/checkPrimers.Rd man/checkConfigFile.Rd man/revComp.Rd man/findEOP.Rd man/getEvents.Rd man/unassignedData-set.Rd man/amplicanReport.Rd man/readCounts-set.Rd man/plot_cuts.Rd man/fwdReadsType.Rd man/get_amplicon.Rd man/comb_along.Rd man/geom_bezier.Rd man/cumsumw.Rd man/get_right_primer.Rd man/amplican_print_reads.Rd man/cigarsToEvents.Rd man/amplicanPipelineConservative.Rd man/plot_insertions.Rd man/makeAlignment.Rd man/amplicanFilter.Rd man/lookupAlignment.Rd man/unassignedData.Rd man/metaplot_insertions.Rd man/rveReadsType-set.Rd man/alphabetQuality.Rd man/get_left_primer.Rd man/metaplot_deletions.Rd man/rveReadsType.Rd man/unassignedCount.Rd man/findPD.Rd man/barcodeData.Rd man/extractEvents.Rd man/metaplot_mismatches.Rd tests/testthat.R tests/testthat/test_filters_helpers.R tests/testthat/test_plot_helpers.R tests/testthat/test_general_helpers.R tests/testthat/test_alignment_helpers.R tests/testthat/test_summary_helpers.R tests/testthat/test_amplican.R

inst/TODO

inst/NEWS

inst/CITATION

inst/doc/example_amplicon_report.html

inst/doc/example_id_report.Rmd inst/doc/example_barcode_report.Rmd inst/doc/example_amplicon_report.R inst/doc/example_group_report.Rmd inst/doc/example_barcode_report.R inst/doc/example_group_report.R inst/doc/amplicanOverview.R inst/doc/amplicanFAQ.Rmd inst/doc/example_index.R

inst/doc/example_guide_report.html

inst/doc/example_group_report.html

inst/doc/amplicanOverview.html

inst/doc/example_id_report.html

inst/doc/example_index.html

inst/doc/example_guide_report.R inst/doc/example_amplicon_report.Rmd

inst/doc/example_barcode_report.html

inst/doc/example_index.Rmd inst/doc/example_id_report.R inst/doc/amplicanOverview.Rmd

inst/doc/amplicanFAQ.html

inst/doc/example_guide_report.Rmd

inst/test_data/test_cfg.csv

inst/test_data/test_aln.csv

inst/extdata/R1_001.fastq

inst/extdata/config.csv

inst/extdata/R2_002.fastq

inst/extdata/R1_002.fastq

inst/extdata/R2_001.fastq

inst/extdata/results/RunParameters.txt

inst/extdata/results/config_summary.csv

inst/extdata/results/barcode_reads_filters.csv

inst/extdata/results/alignments/events_filtered_shifted.csv

inst/extdata/results/alignments/events_filtered_shifted_normalized.csv

inst/extdata/results/alignments/unassigned_reads.csv

inst/extdata/results/alignments/raw_events.csv

inst/extdata/results/alignments/alignments.txt

inst/extdata/results/alignments/AlignmentsExperimentSet.rds

inst/rmarkdown/templates/id_report/template.yaml

inst/rmarkdown/templates/id_report/skeleton/skeleton.Rmd

inst/rmarkdown/templates/index_report/template.yaml

inst/rmarkdown/templates/index_report/skeleton/skeleton.Rmd

inst/rmarkdown/templates/group_report/template.yaml

inst/rmarkdown/templates/group_report/skeleton/skeleton.Rmd

inst/rmarkdown/templates/barcode_report/template.yaml

inst/rmarkdown/templates/barcode_report/skeleton/skeleton.Rmd

inst/rmarkdown/templates/guide_report/template.yaml

inst/rmarkdown/templates/guide_report/skeleton/skeleton.Rmd

inst/rmarkdown/templates/amplicon_report/template.yaml

inst/rmarkdown/templates/amplicon_report/skeleton/skeleton.Rmd

amplican documentation built on Nov. 8, 2020, 11:10 p.m.