The Perl Toolchain Summit needs more sponsors. If your company depends on Perl, please support this very important event.
 / 
Bio-Community-0.001005
River stage zero No dependents
1 ++

Changes for version 0.1.5 - 2014-03-12

  • Bio::Community::next_member is faster and now returns identical objects
  • In generic and unifrac drivers, write member description if available, or ID otherwise
  • Renamed Bio::Tools::RepresentativeIdConverter to Bio::Tools::IdConverter. Renamed the corresponding script from bc_use_repr_id to bc_convert_ids. In both module and script, added support for BLAST tabular files and conversion from member description.
  • Added script bc_add_taxonomy that adds a taxonomic lineage when members have a valid taxonomic ID
  • Rarefaction module and script can now assume an infinite number of bootstrap repetitions

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

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::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

Other files