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@gregcaporaso
gregcaporaso / variability_v_diversity.py
Last active Aug 29, 2015
first pass script for comparing median diversity versus median variability for a given category
View variability_v_diversity.py
#!/usr/bin/env python
# File created on 26 Feb 2014
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2014, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Greg Caporaso"
@gregcaporaso
gregcaporaso / README.md
Last active Aug 29, 2015
exploring using pandas for QIIME mapping files
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Some exploration into how the pandas DataFrame could be a useful underlying representation for QIIME's metadata mapping files.

@gregcaporaso
gregcaporaso / README.md
Last active Aug 29, 2015
quick-and-dirty sortmerna-based consensus taxonomy assigner
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This is a first pass at doing rRNA read assignment with sortmerna. This code is completely untested, but provides the framework for starting to test this as an alternative to QIIME's existing taxonomy assigners.

To use this code you'll need:

  • QIIME 1.8.0 or later
  • scikit-bio (latest GitHub version)
  • The sortmerna binaries in your PATH environment variable.
git clone https://gist.github.com/10506167.git smr-tax
@gregcaporaso
gregcaporaso / simple-illustration.ipynb
Last active Aug 29, 2015
taxa collapsing discrepancy
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@gregcaporaso
gregcaporaso / 180-dev.ipynb
Created Nov 6, 2014
comparison of runtime for single_rarefaction.py in QIIME 1.8.0 and 1.8.0-dev
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@gregcaporaso
gregcaporaso / pynast-reference-comparison.ipynb
Last active Aug 29, 2015
Comparison of using GG 13_8 versus Greengenes core set as the default reference for PyNAST
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@gregcaporaso
gregcaporaso / assignment-5.ipynb
Last active Aug 29, 2015
BIO/CS 290, BIO 599 Assignment 5: Spring 2015
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@gregcaporaso
gregcaporaso / iab-ipynb-to-md.ipynb
Created Jun 17, 2015
Used for gregcaporaso/An-Introduction-to-Applied-Bioinformatics#140 to convert the ipython notebooks to markdown files.
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@gregcaporaso
gregcaporaso / qiime191-or-otus-100-params.txt
Last active Sep 30, 2015
This parameters file can be passed to QIIME 1.9.1's pick_open_reference_otus.py command via the ``-p`` parameter to perform OTU picking at 100% identity. This is a computationally inefficient way to do this, so it may not work with very big data sets. We're working on integrating better approaches.
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