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
bt2_16S_paramsA universal parameter object for Bowtie 2 16S alignment
bt2_missing_paramsA universal parameter object for Bowtie 2 metagenomic...
bt2_regular_paramsA universal parameter object for Bowtie 2 metagenomic or...
check_samtools_existsCheck if samtools exists on the system
combined_headerCreate a combined .bam header
convert_animalculesCreate a multi-assay experiment from MetaScope output for...
convert_animalcules_pathoCreate a multi-assay experiment from PathoScope 2.0 output...
convert_animalcules_silvaCreate a multi-assay experiment from MetaScope output for...
count_matchesCount the number of base lengths in a CIGAR string for a...
download_accessionsDownload indexes required for MetaScope ID and MetaBlast...
download_refseqDownload RefSeq genome libraries
extract_readsHelper function for demultiplexing
filter_hostUse Rsubread to align reads against one or more filter...
filter_host_bowtieUse Rbowtie2 to align reads against one or more filter...
filter_unmapped_readsFilter unmapped reads
get_childrenGet child nodes from NCBI taxonomy
locationsHelper Function for MetaScope ID
merge_bam_filesMerge multiple .bam files
meta_demultiplexDemultiplexing sequencing reads
metascope_idIdentify which genomes are represented in a processed 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
compbiomed/MetaScope documentation built on June 10, 2025, 11:52 a.m.