├── .Rbuildignore ├── .gitignore ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── MetaScope-package.R ├── align_target.R ├── check_samtools_exists.R ├── convert_animalcules.R ├── convert_animalcules_patho.R ├── convert_animalcules_silva.R ├── data.R ├── demultiplex.R ├── download_accessions.R ├── download_refseq.R ├── download_refseq_16S.R ├── filter_host.R ├── get_children.R ├── metascope_blast.R ├── metascope_id.R ├── metascope_inspect.R ├── mk_bowtie_index.R ├── mk_subread_index.R ├── mk_table.R ├── run_metascope.R └── sysdata.rda ├── README.md ├── data-raw ├── align_details.R ├── bt2_16S_params.R ├── bt2_missing_params.R ├── bt2_regular_params.R ├── correct_silva_headers.R ├── generate_example_accessions.R └── generate_taxonomy_table.R ├── data ├── align_details.rda ├── bt2_16S_params.rda ├── bt2_missing_params.rda └── bt2_regular_params.rda ├── index.md ├── inst ├── WORDLIST ├── bowtie2-inspect ├── bowtie2-inspect-l ├── bowtie2-inspect-l-debug ├── bowtie2-inspect-s ├── bowtie2-inspect-s-debug ├── extdata │ ├── barcodes.txt │ ├── bowtie_target.bam │ ├── bowtie_target.filtered.csv.gz │ ├── example_accessions.sql │ ├── reads.fastq │ ├── subread_target.bam │ ├── subread_target.filtered.csv.gz │ ├── virus_example.fastq │ └── virus_example_index.fastq └── script │ └── extdata_explanations.Rmd ├── man ├── MetaScope-package.Rd ├── add_in_taxa.Rd ├── add_in_taxa_ncbi.Rd ├── align_details.Rd ├── align_target.Rd ├── align_target_bowtie.Rd ├── bam_reheader_R.Rd ├── blast_reassignment.Rd ├── blast_result_metrics.Rd ├── blastn_results.Rd ├── blastn_single_result.Rd ├── bt2_16S_params.Rd ├── bt2_missing_params.Rd ├── bt2_regular_params.Rd ├── check_blastn_exists.Rd ├── check_samtools_exists.Rd ├── combined_header.Rd ├── convert_animalcules.Rd ├── convert_animalcules_patho.Rd ├── convert_animalcules_silva.Rd ├── count_matches.Rd ├── download_accessions.Rd ├── download_refseq.Rd ├── download_refseq_16S.Rd ├── extract_reads.Rd ├── filter_host.Rd ├── filter_host_bowtie.Rd ├── filter_unmapped_reads.Rd ├── find_taxids.Rd ├── get_children.Rd ├── get_multi_seqs.Rd ├── get_seqs.Rd ├── locations.Rd ├── merge_bam_files.Rd ├── meta_demultiplex.Rd ├── metascope_blast.Rd ├── metascope_id.Rd ├── metascope_inspect.Rd ├── metascope_inspect_usage.Rd ├── mk_bowtie_index.Rd ├── mk_subread_index.Rd ├── remove_matches.Rd ├── run_metascope.Rd └── taxid_to_name.Rd ├── pkgdown └── _pkgdown.yml ├── tests └── spelling.R └── vignettes ├── MetaScope_Workflow.png ├── MetaScope_vignette.Rmd └── vignette_docs ├── Example_Script.Rmd ├── SILVA.Rmd └── publicly_hosted_indices_and_accessions.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wejlab/MetaScope/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: 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