Man pages for compbiomed/MetaScope
Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

align_detailsA universal parameter settings object for Rsubread alignment
align_targetAlign microbiome reads to a set of reference libraries
align_target_bowtieAlign microbiome reads to set of indexed Bowtie2 libraries
bam_reheader_RReplace the header from a .bam file
combined_headerCreate a combined .bam header
convert_animalculesCreate a multi-assay experiment from MetaScope output for...
count_matchesCount the number of base lengths in a CIGAR string for a...
demultiplexDemultiplexing sequencing reads
download_refseqDownload RefSeq genome libraries
extractReadsHelper function for demultiplexing
filter_hostAlign reads against one or more filter libraries and...
filter_host_bowtieAlign reads against one or more filter libraries and...
filter_unmapped_readsFilter unmapped reads
generate_taxonomy_tableGenerate the taxonomy table
get_childrenGet child nodes from NCBI taxonomy
locationsHelper Function for MetaScope ID
merge_bam_filesMerge multiple .bam files
metascope_idIdentify which genomes are represented in a sample
MetaScope-packageMetaScope: Tools and functions for preprocessing 16S and...
mk_bowtie_indexMake a Bowtie2 index
mk_subread_indexMake a Subread index
remove_matchesHelper function to remove reads matched to filter libraries
taxonomy_tableTaxonomy table
compbiomed/MetaScope documentation built on Aug. 9, 2022, 10:41 a.m.