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ag-plots

american-gut

American Gut open-access data and IPython notebooks

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

bioparse

Module for parsing the output of various bioinformatics tools.

biotm

Biom tables meet topic models. Topic models meet biom tables.

classification

Benchmarking classification techniques

coassembly

Generate coassembly test cases

example_project

demo

faculty_hiring

University faculty hiring analysis

faculty_productivity

gene-coverage

Report largest fraction of coverage.

machine-learning

Playground for learning about and evaluating machine learning techniques.

make_figures_great_again

MAKE FIGURES GREAT AGAIN

ml_utils

Utility scripts for interfacing QIIME with scikit-learn.

pipeline_lite

Generates scripts to run a basic sequencing pipeline.

python_to_slda

Scripts for interfacing biom tables and metadata files with slda

qiime-deploy

Tool to easily install QIIME on Linux systems

qiime-deploy-conf

configuration files to be used with the qiime-deploy packages

qiime-scaling

The goal of this project is to produce an estimator for runtime and memory consumption: (runtime, memory) = f(script_name, number_of_observations, number_of_samples, sparsity). This estimator will be based off of empirical results from standard test data sets (to be created, described below) and validated with real world datasets. Once in place, we can then use this estimator to a) improve resource utilization on both growler and compy b) determine what scripts to target for optimization.

redblue

Analysis of Halo Reach data

research_env

Analysis of how academic environment affects individual researcher productivity.

samplotlib

matplotlib hacks

scholar.py

A parser for Google Scholar, written in Python

trees

Predicting forest cover

university_network

Code to analyze faculty hiring at North American universities.