Files in valenlab/amplican
Automated analysis of CRISPR experiments

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/AlignmentsExperimentSet-class.R R/amplican.R R/amplicanAlign.R R/amplicanFilter.R R/amplicanNormalize.R R/amplicanReport.R R/amplicanSummarize.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
amplican.Rproj
inst/NEWS
inst/TODO
inst/extdata/R1_001.fastq
inst/extdata/R1_002.fastq
inst/extdata/R2_001.fastq
inst/extdata/R2_002.fastq
inst/extdata/config.csv
inst/extdata/results/RunParameters.txt
inst/extdata/results/alignments/AlignmentsExperimentSet.rds
inst/extdata/results/alignments/alignments.txt
inst/extdata/results/alignments/events_filtered_shifted.csv
inst/extdata/results/alignments/events_filtered_shifted_normalized.csv
inst/extdata/results/alignments/raw_events.csv
inst/extdata/results/alignments/unassigned_reads.csv
inst/extdata/results/barcode_reads_filters.csv
inst/extdata/results/config_summary.csv
inst/rmarkdown/templates/amplicon_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/amplicon_report/template.yaml
inst/rmarkdown/templates/barcode_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/barcode_report/template.yaml
inst/rmarkdown/templates/group_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/group_report/template.yaml
inst/rmarkdown/templates/guide_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/guide_report/template.yaml
inst/rmarkdown/templates/id_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/id_report/template.yaml
inst/rmarkdown/templates/index_report/skeleton/skeleton.Rmd
inst/rmarkdown/templates/index_report/template.yaml
inst/test_data/test_aln.csv
inst/test_data/test_cfg.csv
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/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/getEventInfo.Rd man/getEvents.Rd man/get_amplicon.Rd man/get_left_primer.Rd man/get_right_primer.Rd man/goodAvgQuality.Rd man/goodBaseQuality.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/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/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
vignettes/figures/amplican_conceptual_map.png
vignettes/figures/amplican_consensus_rules.png
valenlab/amplican documentation built on June 18, 2018, 6:04 a.m.