Bio::Community - A biological community River stage zero No dependents

The Bio::Community module represents communities of biological organisms. It is composed of Bio::Community::Member objects at a specified abundance. Each member can represent a species (e.g. an elephant, a bacterium), taxon, OTU, or any proxy for a s...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::IO - Read and write files that describe communities River stage zero No dependents

A Bio::Community::IO object implement methods to read and write communities in formats used by popular programs such as BIOM, GAAS, QIIME, Unifrac, or as generic tab-separated tables. The format should be automatically detected though it can be manua...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Meta - A metacommunity, or group of communities River stage zero No dependents

The Bio::Community::Meta module represent metacommunities, or groups of communities. This object holds several Bio::Community objects, for example tree communities found at different sites of a forest. Random access to any of the communities is provi...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Types - Data type definitions River stage zero No dependents

This module defines useful data types for use in Moose-based modules....

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Alpha - Calculate the alpha diversity of a community River stage zero No dependents

The Bio::Community::Alpha module calculates alpha diversity, i.e. the diversity contained within a community. Higer alpha diversity values indicate more diverse communities....

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Member - The basic constituent of a biological community River stage zero No dependents

A Bio::Community::Member represents an organism, individual, species, amplicon sequence, shotgun sequence or anything you like....

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Role::IO - Role for IO layer River stage zero No dependents

This role is an IO layer to read and write community files. The only thing it does is define methods that the role-consuming class must implement. In practice, this role is should be used by all the IO drivers in the Bio::Community::IO::* namespace. ...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Role::PRNG - Role for objects that use a pseudo-random number generator River stage zero No dependents

This role provides the capability to generate random numbers using a specified or automatically determined seed. This module uses the superior Mersenne-Twister algorithm provided by the Math::GSL::RNG module to draw uniformly distributed random numbe...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Meta::Beta - Beta diversity or distance separating communities River stage zero No dependents

The Bio::Community::Beta module quantifies how dissimilar communities are by calculating their beta diversity. The more different communities are, the larger their beta diversity. Some beta diversity metrics are proper distance measures (in the mathe...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Role::Table - Role to read/write data tables and provide random access to their cells River stage zero No dependents

This role implements methods to read and write file structured as a table containing rows and columns. When reading a table from a file, an index is kept to provide random-access to any cell of the table. When writing a table to a file, cell data can...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Meta::Gamma - Calculate the gamma diversity of a metacommunity River stage zero No dependents

The Bio::Community::Meta::Gamma module calculates the gamma diversity of a group of communities (provided as a metacommunity object). Higer gamma diversity values indicate more diverse metacommunities....

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Role::Locked - Role for objects that can be locked (made read-only) River stage zero No dependents

This role provides the capability to make objects of the class that consumes this role read-only. The lock() method can be invoked to make an object read-only, while unlock() restores the read/write properties of the object. If you try to call a meth...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::TaxonomyUtils - Functions for manipulating taxonomic lineages River stage zero No dependents

This module implements functions to manipulate taxonomic lineages, as arrayref of taxon names or taxon objects....

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Tools::Sampler - Sample organisms according to their abundance River stage zero No dependents

Pick individuals at random (without replacement) from a community. Note that the sampling is done based on relative abundances, and is hence affected by weights. If you need to sample based on counts instead, simply set $community->use_weights(0), be...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Role::Weighted - Role for objects that have a weight River stage zero No dependents

This role provides the capability to add an arrayref of weights (strictly positive numbers) to objects of the class that consumes this role....

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Role::Sequenced - Role for objects that have a sequence River stage zero No dependents

This role provides the capability to add an arrayref of sequences (Bio::PrimarySeq compliant objects) to objects of the class that consumes this role....

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Role::Described - Role for objects that have a description River stage zero No dependents

This role provides the capability to add an arbitrary description (a string) to objects of the class that consumes this role....

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Tools::Rarefier - Normalize communities by count River stage zero No dependents

This module takes a metacommunity and normalizes (rarefies) the communities it contains by their number of counts. Comparing the composition and diversity of biological communities can be biased by sampling artefacts. When comparing two identical com...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::IO::Driver::gaas - Driver to read and write files in the GAAS format River stage zero No dependents

This Bio::Community::IO::Driver::gaas driver reads and writes files in the format generated by GAAS (http://sourceforge.net/projects/gaas/). GAAS creates one such file per community. Here is an example: # tax_name tax_id rel_abund Streptococcus pyoge...

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

Bio::Community::Role::Classified - Role for objects that have a taxonomic classification River stage zero No dependents

This role provides the capability to add a taxonomic classification (Bio::Taxon object) to objects of the class that consumes this role....

FANGLY/Bio-Community-0.001008 - 08 Jan 2016 20:06:45 GMT

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