OTU_table

require(GCModeller); {$desc_comments} imports "OTU_table" from "metagenomics_kit";

.NET clr type export
OTU_table: OTUTable	OTU table (sequence count table) A OTU table contains the number of sequences that are observed for each taxonomic unit (OTUs) in each samples. Columns usually represent samples and rows represent genera or species specific taxonomic units (OTUs). OTU tables are often saved as BIOM formatted files. Limited taxonomic resolution OTU resolution depends On the 16S approach which has some limits In distinguishing at the species level, For example, Escherichia coli And Shigella spp. share almost identical 16S rRNA gene sequences. Alternative approaches are developed To achieve higher resolution up To strain level by considering larger Or complete sets Of genes.

.NET clr function exports
as.data.frame.otutable	OTUTable: OTU table (sequence count table) A OTU table contains the number of sequences that are observed for each taxonomic unit (OTUs) in each samples. Columns usually represent samples and rows represent genera or species specific taxonomic units (OTUs). OTU tables are often saved as BIOM formatted files. Limited taxonomic resolution OTU resolution depends On the 16S approach which has some limits In distinguishing at the species level, For example, Escherichia coli And Shigella spp. share almost identical 16S rRNA gene sequences. Alternative approaches are developed To achieve higher resolution up To strain level by considering larger Or complete sets Of genes.
sample_id
relative_abundance
average
median_scale
filter
read.OTUtable
read.OTUdata
otu_from_matrix
as.hts_matrix
read.rankdata
as.OTU_table
set_MAG_data
set_taxonomyName
core_microbiome
dominant_species
make_otu_table
makeTreeGraph
makeUPGMATree
drawUPGMATree
make_repseq_id
merge_phyloseq
batch_combine