Files in compbiomed/MetaScope
Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data
.Rbuildignore
.gitignore
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/MetaScope-package.R
R/align_target.R
R/check_samtools_exists.R
R/convert_animalcules.R
R/convert_animalcules_patho.R
R/convert_animalcules_silva.R
R/data.R
R/demultiplex.R
R/download_refseq.R
R/filter_host.R
R/get_children.R
R/metascope_blast.R
R/metascope_id.R
R/mk_bowtie_index.R
R/mk_subread_index.R
R/mk_table.R
R/sysdata.rda
README.md
data-raw/align_details.R
data-raw/bt2_16S_params.R
data-raw/bt2_missing_params.R
data-raw/bt2_regular_params.R
data-raw/correct_silva_headers.R
data-raw/generate_taxonomy_table.R
data/align_details.rda
data/bt2_16S_params.rda
data/bt2_missing_params.rda
data/bt2_regular_params.rda
index.md
inst/WORDLIST
inst/extdata/barcodes.txt
inst/extdata/bowtie_target.bam
inst/extdata/bowtie_target.filtered.csv.gz
inst/extdata/reads.fastq
inst/extdata/subread_target.bam
inst/extdata/subread_target.filtered.csv.gz
inst/extdata/virus_example.fastq
inst/extdata/virus_example_index.fastq
inst/script/extdata_explanations.Rmd
man/MetaScope-package.Rd
man/add_in_taxa.Rd
man/add_in_taxa_ncbi.Rd
man/align_details.Rd
man/align_target.Rd
man/align_target_bowtie.Rd
man/bam_reheader_R.Rd
man/blast_reassignment.Rd
man/blast_result_metrics.Rd
man/blastn_results.Rd
man/blastn_single_result.Rd
man/bt2_16S_params.Rd
man/bt2_missing_params.Rd
man/bt2_regular_params.Rd
man/check_blastn_exists.Rd
man/check_samtools_exists.Rd
man/combined_header.Rd
man/convert_animalcules.Rd
man/convert_animalcules_patho.Rd
man/convert_animalcules_silva.Rd
man/count_matches.Rd
man/download_refseq.Rd
man/extract_reads.Rd
man/filter_host.Rd
man/filter_host_bowtie.Rd
man/filter_unmapped_reads.Rd
man/get_children.Rd
man/get_multi_seqs.Rd
man/get_seqs.Rd
man/locations.Rd
man/merge_bam_files.Rd
man/meta_demultiplex.Rd
man/metascope_blast.Rd
man/metascope_id.Rd
man/mk_bowtie_index.Rd
man/mk_subread_index.Rd
man/remove_matches.Rd
man/taxid_to_name.Rd
pkgdown/_pkgdown.yml
tests/spelling.R
vignettes/MetaScopeTutorial.Rmd
vignettes/MetaScope_Workflow.png
vignettes/MetaScope_vignette.Rmd
