Florent Angly > Bio-Community-0.001005

Bio-Community-0.001005

This Release Bio-Community-0.001005  [Download] [Browse 12 Mar 2014
Latest Release Bio-Community-0.001007  [Download] [Browse 27 May 2014
Other Releases
Links Discussion Forum ] [ View/Report Bugs ] [ Website ] [ Dependencies ] [ Other Tools ]
Repository git://github.com/bioperl/Bio-Community.git
CPAN Testers PASS (34)   FAIL (2)   NA (5)   [ View Reports ] [ Perl/Platform Version Matrix ]
Rating      (0 Reviews) [ Rate this distribution ]
License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
Build.PL
Changes
LICENSE
MANIFEST
META.json
README

Modules

Bio::Community A biological community     0.001005
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::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      

Documentation

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_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