46 results (0.166 seconds)
Florent Angly
Documentation
bc_accumulate - Create species accumulation curves (collector or rarefaction)
bc_add_taxonomy - Add a taxonomic lineage to community members
bc_clean_shrapnel - Remove low-count, low-prevalence community members
bc_convert_files - Merge/split community files and convert between formats
bc_convert_ids - Convert member ID from member attribute or file
bc_correct_mis_assignments - Try fixing incorrect taxonomic assignments, using a reference community
bc_get_info - Get information about a community file
bc_manage_members - Delete or rename community members
bc_manage_samples - Include, delete, merge, sort or rename samples
bc_measure_alpha - Measure alpha diversity of communities
bc_measure_beta - Measure beta diversity between communities
bc_rarefy - Rarefy communities
bc_relative_to_absolute - Convert relative abundances into absolute
bc_remove_unexpected_members - Remove community members not expected to occur, based on a reference community
bc_summarize - Summarize community composition
Modules
Bio::Community - A biological community
Bio::Community::Alpha - Calculate the alpha diversity of a community
Bio::Community::IO - Read and write files that describe communities
Bio::Community::IO::Driver::biom - Driver to read and write files in the sparse BIOM format
Bio::Community::IO::Driver::dummy - Dummy driver (does nothing)
Bio::Community::IO::Driver::gaas - Driver to read and write files in the GAAS format
Bio::Community::IO::Driver::generic - Driver to read and write files in a generic tab-delimited site-by-species table format
Bio::Community::IO::Driver::qiime - Driver to read and write files in the QIIME format
Bio::Community::IO::Driver::unifrac - Driver to read and write files in the (Fast)Unifrac format
Bio::Community::IO::FormatGuesser - Determine the format used by a community file
Bio::Community::Member - The basic constituent of a biological community
Bio::Community::Meta - A metacommunity, or group of communities
Bio::Community::Meta::Beta - Beta diversity or distance separating communities
Bio::Community::Meta::Gamma - Calculate the gamma diversity of a metacommunity
Bio::Community::Role::Classified - Role for objects that have a taxonomic classification
Bio::Community::Role::Described - Role for objects that have a description
Bio::Community::Role::IO - Role for IO layer
Bio::Community::Role::Locked - Role for objects that can be locked (made read-only)
Bio::Community::Role::PRNG - Role for objects that use a pseudo-random number generator
Bio::Community::Role::Sequenced - Role for objects that have a sequence
Bio::Community::Role::Table - Role to read/write data tables and provide random access to their cells
Bio::Community::Role::Weighted - Role for objects that have a weight
Bio::Community::TaxonomyUtils - Functions for manipulating taxonomic lineages
Bio::Community::Tools::Accumulator - Species accumulation curves
Bio::Community::Tools::IdConverter - Various methods to convert member ID
Bio::Community::Tools::Rarefier - Normalize communities by count
Bio::Community::Tools::Sampler - Sample organisms according to their abundance
Bio::Community::Tools::ShrapnelCleaner - Remove low-count, low-abundance community members
Bio::Community::Tools::Summarizer - Create a summary of communities
Bio::Community::Tools::Transformer - Arbitrary transformation of member counts
Bio::Community::Types - Data type definitions



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