PySurvey

HomePage: UNKNOWN

Author: Jonathan Friedman

Download: https://pypi.python.org/packages/source/P/PySurvey/PySurvey-0.1.2.tar.gz

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PySurvey: Interactive analysis of survey data 
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``PySurvey`` is a `Python <http://www.python.org>`__ package designed to perform interactive analysis of survey data, composed of counts of occurrence of different categories in a collection of samples. 
Specifically, ``PySurvey`` is developed in the context of genomic surveys, such as 16S surveys, where one studies the occurrence of OTUs across samples.
Though much of ``PySurvey``'s functionality is not unique to survey data, and equivalent features are implemented in many other packages, ``PySurvey`` is intended to serve as a 'one-stop-shop', and thus attempts to includes all the methods that are commonly used in the analysis of genomic survey data (often by wrapping around other packages), with a sensible choice of default parameters (e.g. distance metrics, etc').

``PySurvey`` is based on the powerful `pandas <http://pandas.pydata.org/>`__ package which offers rich data structures which are 
tailored and optimized for interactive analysis of large data tables.

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``PySurvey`` Resources
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- **Documentation:** http://yonatanfriedman.com/docs/survey/index.html
- **Source Repository:** https://bitbucket.org/yonatanf/pysurvey


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Key Features
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  - General utility:
	- Metadata support.
	- Filtering of samples/components.
	- ML and Bayesian estimation of component fractions.

  - Exploratory analysis:
	- Dimension reduction: PCoA.
	- Clustering: hierarchical, gaussian mixture models GMM.
	- Compositional correlations via `SparCC <https://bitbucket.org/yonatanf/sparcc>`__.
	- Plotting: sorted heatmaps, stacked plots, ...
  
  - Ecological theory:
  	- Sample diversities (alpha diversity).	
	- Rarefaction.
  	- Rank abundance plots.