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adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

algs4

Princeton's COS226

ascatngsutils

Extract `logR` and `BAF` from BAM files.

fun

Ad-hoc fun projects whose state of doneness is likely in [0,1)

graphicalmodel

Courera Version of Graphical Model.. Cooperate with Jian Guo.

guacamole

Simple Spark-based variant calling

inferelator_ng

Inferelator refactor and generalization.

instagram-news-cli

A quick and dirty hack to read you Instagram news feed from the command line

iphone-sms-backup

Backup your iPhone SMS text messages.

manspeak

opera_db

pgmpy

Python Library for Probabilistic Graphical Models

phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.

probability_cheatsheet

A comprehensive 8-page probability cheatsheet that covers a semester's worth of introduction to probability.

pytcga

Store and query public TCGA data

reference-apps

Spark reference applications

scholar.py

A parser for Google Scholar, written in Python

scipy_proceedings

Tools used to generate the SciPy conference proceedings

secotrec

Setup Coclobas/Ketrew Clusters

spark-timeseries

A library for financial and time series calculations on Apache Spark

splash

Splash Project for parallel stochastic learning

stancache

Filecache for stan models

stanford_corenlp_py

stray

Multinomial Logistic-Normal Linear Regression Models

thresholdout

Mirror of the scripts for Dwork et al's paper on holdout reuse

wholecell

Mycoplasma genitalium whole-cell model