Files in compbiomed/MetaScope
Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

.Rbuildignore
CODE_OF_CONDUCT.md
DESCRIPTION
NAMESPACE
NEWS.md R/MetaScope-package.R R/MetaScope_ID.R R/align_target.R R/convert_animalcules.R R/data.R R/demultiplex.R R/download_refseq.R R/filter_host.R R/generate_taxonomy_table.R R/get_children.R R/mk_bowtie_index.R R/mk_subread_index.R
R/sysdata.rda
README.md data-raw/align_details.R
data/align_details.rda
index.md
inst/WORDLIST
inst/extdata/DATA_README.txt
inst/extdata/barcodes.txt
inst/extdata/bowtie_target.bam
inst/extdata/bowtie_target.filtered.bam
inst/extdata/bowtie_target.filtered.metascope_id.csv
inst/extdata/filter.fasta
inst/extdata/reads.fastq
inst/extdata/subread_target.bam
inst/extdata/subread_target.filtered.bam
inst/extdata/target.fasta
inst/extdata/virus_example.fastq
inst/extdata/virus_example_index.fastq
inst/shiny/All_Code_App.Rmd inst/shiny/UI/UI_align_target.R inst/shiny/UI/UI_demultiplex.R inst/shiny/UI/UI_ref_seq.R inst/shiny/UI/UI_ref_seq_2.R inst/shiny/animalcule_preprocess_app.R inst/shiny/server/server_demultiplex.R inst/shiny/server/server_ref_seq.R inst/shiny/ui_01_demultiplex.R man/MetaScope-package.Rd man/align_details.Rd man/align_target.Rd man/align_target_bowtie.Rd man/bam_reheader_R.Rd man/combined_header.Rd man/convert_animalcules.Rd man/count_matches.Rd man/demultiplex.Rd man/download_refseq.Rd man/extractReads.Rd man/filter_host.Rd man/filter_host_bowtie.Rd man/filter_unmapped_reads.Rd man/generate_taxonomy_table.Rd man/get_children.Rd man/locations.Rd man/merge_bam_files.Rd man/metascope_id.Rd man/mk_bowtie_index.Rd man/mk_subread_index.Rd man/remove_matches.Rd man/taxonomy_table.Rd
pkgdown/_pkgdown.yml
tests/package_coverage.R tests/spelling.R tests/testthat.R tests/testthat/test-lintr.R vignettes/MetaScope_vignette.Rmd vignettes/rmd/oldMetascope_vignette.Rmd
vignettes/rmd/workflow_patho.png
compbiomed/MetaScope documentation built on Aug. 9, 2022, 10:41 a.m.