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py_peak_calling

Simple threshold based peak calling for ChIP style data

python-suffix-tree

Suffix tree for string searching

python_pcoa

The Python implementation for Principal Coordinate Analysis

pyvcf

A Variant Call Format reader for Python.

q2-feature-classifier

QIIME 2 plugin supporting taxonomic classification

q2-phylogeny

Multiple sequence alignment, phylogenetic reconstruction, and operations on phylogenetic trees.

q2studio

A web interface for QIIME 2

qiime

Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests

qiime-galaxy

Repository for QIIME/Galaxy integration code.

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.

qiime2

Official repository for the QIIME 2 framework

qiime_test_data

Test input and output for QIIME scripts.

qiime_to_lefse

Convert Qiime taxa tables and mapping files to a lefse formatted file

qiimebyjennomics

IPython notebook for microbial ecology analysis in QIIME

qiimeintegration

I'm working on incorporating QIIME into a workspace-specific pipeline. I keep notes and useful scripts here.

qiita

Qiita - A QIIME databasing effort

qmp

Quantitative Microbiome Profiling

qpcr

Code for qPCR analysis

qpcr-1

Primer design and qPCR analysis

quartz-wm

The quartz-wm window manager for XQuartz

r

Exercises with R language (math+statistics)

r-ecology-lesson

Data Carpentry R lessons on ecology

r-intermediate-altmetrics

A 2-day workshop on intermediate-level programming with R

r4ds

R for data science

raceid

ramp

Rapid Machine Learning Prototyping in Python

random-forest

Randomized Decision Trees: A Fast C++ Implementation of Random Forests.

randomforest

:exclamation: This is a read-only mirror of the CRAN R package repository. randomForest — Breiman and Cutler's Random Forests for Classification and Regression. Homepage: https://www.stat.berkeley.edu/~breiman/RandomForests/

rarefaction

Rarefaction scripts

rbmpaper

experiments and datasets used for the paper "A Deep Learning Approach to Unsupervised Ensemble Learning"