Files in lerch-a/HaplotypR
HaplotypR, a pipeline to analyse amplicon deep sequencing genotyping data
.github/workflows/R-CMD-check.yml
DESCRIPTION
LICENSE
NAMESPACE
R/appFunction.R
R/callGenotype.R
R/callHaplotype.R
R/callHaplotypeDADA2.R
R/clusterFunction.R
R/filterHaplotype.R
R/haplotyperProject.R
R/helperFunction.R
R/minION_function.R
R/plotFunctions.R
R/processReads.R
docs/README.md
docs/README_new.md
docs/_config.yml
docs/_layouts/default.html
docs/documentation/bindReads.md
docs/documentation/index.md
docs/documentation/makeInputFiles.md
docs/documentation/makePrimerFile.md
docs/documentation/mergeReads.md
docs/documentation/minIonDR_workflow.md
docs/documentation/minIon_workflow.md
docs/foo.md
inst/CITATION
inst/extdata/barcode_Fwd.fasta
inst/extdata/barcode_Rev.fasta
inst/extdata/ex2/barcode_F.fasta
inst/extdata/ex2/barcode_R.fasta
inst/extdata/ex2/marker_file.txt
inst/extdata/ex2/reads2_F.fastq.gz
inst/extdata/ex2/reads2_R.fastq.gz
inst/extdata/ex2/sample_file.txt
inst/extdata/ex3/MH_ama1_D2_18.fasta
inst/extdata/ex3/MH_celtos.fasta
inst/extdata/ex3/MH_cpmp_22.fasta
inst/extdata/ex3/MH_cpp_30.fasta
inst/extdata/ex3/MH_csp_27.fasta
inst/extdata/ex3/MH_surfin1_1.fasta
inst/extdata/ex3/marker_file_ex3.txt
inst/extdata/ex3/mutationList.txt
inst/extdata/ex3/read_dir_ex3/barcode01/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode01.fastq
inst/extdata/ex3/read_dir_ex3/barcode02/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode02.fastq
inst/extdata/ex3/read_dir_ex3/barcode03/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode03.fastq
inst/extdata/ex3/read_dir_ex3/barcode04/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode04.fastq
inst/extdata/ex3/read_dir_ex3/barcode05/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode05.fastq
inst/extdata/ex3/read_dir_ex3/barcode06/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode06.fastq
inst/extdata/ex3/read_dir_ex3/barcode07/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode07.fastq
inst/extdata/ex3/read_dir_ex3/barcode08/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode08.fastq
inst/extdata/ex3/read_dir_ex3/barcode09/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode09.fastq
inst/extdata/ex3/read_dir_ex3/barcode10/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode10.fastq
inst/extdata/ex3/read_dir_ex3/barcode11/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode11.fastq
inst/extdata/ex3/read_dir_ex3/barcode12/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode12.fastq
inst/extdata/ex3/read_dir_ex3/barcode13/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode13.fastq
inst/extdata/ex3/read_dir_ex3/barcode14/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode14.fastq
inst/extdata/ex3/read_dir_ex3/barcode15/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode15.fastq
inst/extdata/ex3/read_dir_ex3/barcode16/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode16.fastq
inst/extdata/ex3/read_dir_ex3/barcode17/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode17.fastq
inst/extdata/ex3/read_dir_ex3/barcode18/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode18.fastq
inst/extdata/ex3/read_dir_ex3/barcode19/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode19.fastq
inst/extdata/ex3/read_dir_ex3/barcode20/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode20.fastq
inst/extdata/ex3/read_dir_ex3/barcode21/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode21.fastq
inst/extdata/ex3/read_dir_ex3/barcode22/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode22.fastq
inst/extdata/ex3/read_dir_ex3/barcode23/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode23.fastq
inst/extdata/ex3/read_dir_ex3/barcode25/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode25.fastq
inst/extdata/ex3/read_dir_ex3/barcode26/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode26.fastq
inst/extdata/ex3/read_dir_ex3/barcode27/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode27.fastq
inst/extdata/ex3/read_dir_ex3/barcode28/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode28.fastq
inst/extdata/ex3/read_dir_ex3/barcode29/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode29.fastq
inst/extdata/ex3/read_dir_ex3/barcode30/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode30.fastq
inst/extdata/ex3/read_dir_ex3/barcode31/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode31.fastq
inst/extdata/ex3/read_dir_ex3/barcode32/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode32.fastq
inst/extdata/ex3/read_dir_ex3/barcode33/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode33.fastq
inst/extdata/ex3/read_dir_ex3/barcode34/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode34.fastq
inst/extdata/ex3/read_dir_ex3/barcode35/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode35.fastq
inst/extdata/ex3/read_dir_ex3/barcode36/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode36.fastq
inst/extdata/ex3/read_dir_ex3/barcode37/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode37.fastq
inst/extdata/ex3/read_dir_ex3/barcode38/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode38.fastq
inst/extdata/ex3/read_dir_ex3/barcode39/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode39.fastq
inst/extdata/ex3/read_dir_ex3/barcode40/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode40.fastq
inst/extdata/ex3/read_dir_ex3/barcode41/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode41.fastq
inst/extdata/ex3/read_dir_ex3/barcode42/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode42.fastq
inst/extdata/ex3/read_dir_ex3/barcode43/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode43.fastq
inst/extdata/ex3/read_dir_ex3/barcode44/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode44.fastq
inst/extdata/ex3/read_dir_ex3/barcode45/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode45.fastq
inst/extdata/ex3/read_dir_ex3/barcode46/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode46.fastq
inst/extdata/ex3/read_dir_ex3/barcode47/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode47.fastq
inst/extdata/ex3/read_dir_ex3/barcode73/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode73.fastq
inst/extdata/ex3/read_dir_ex3/barcode74/2f95113f72cfa054edddabd46534b254380cc780_SQK-NBD114-96_barcode74.fastq
inst/extdata/ex3/sample_file_ex3.txt
inst/extdata/markerFile.txt
inst/extdata/readsF.fastq.gz
inst/extdata/readsR.fastq.gz
inst/extdata/sampleFile.txt
inst/shinyApp/app.R
inst/shinyApp/guiHelper.R
inst/shinyApp/serverHelper.R
inst/shinyApp/www/haplotypRstyle.css
vignettes/HaplotypR-refs.bib
vignettes/HaplotypR.Rnw
