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puppet-playground

A Vagrant MultiOS environment to test Puppet code and modules

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

pyston

An open-source Python implementation using JIT techniques.

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

pytorch-lightning

The lightweight PyTorch wrapper for high-performance AI research. Scale your models, not the boilerplate.

pytorch-optimizer

torch-optimizer -- collection of optimizers for Pytorch

quora_querstion_pairs_kaggle

quotebookr

Automatically exported from code.google.com/p/quotebookr

re-pair

Program to re-do the pairing of fastq reads. This program is modified from http://code.google.com/p/ngopt/source/browse/trunk/tools/pair_reads/repair.cpp?r=85

rmate

rust-seqprep

scvi-dev

Development branch of the scVI project in PyTorch

seizure-detection

Kaggle competition winning submission for the UPenn and Mayo Clinic's Seizure Detection Challenge

seqprep

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

signalstepdetector

Automatically exported from code.google.com/p/signalstepdetector

simseq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.

starcluster

StarCluster is a utility for creating and managing computing clusters hosted on Amazon's Elastic Compute Cloud (EC2).

swift-c-htslib

Ultra-light HTSLIB wrapper for swift, currently just a modulemap giving you access to the C functions.

swift-c-htslib-example

Example swift package built against CHTSLib

textmate

TextMate is a graphical text editor for OS X 10.7+

x-transformers

A simple but complete full-attention transformer with a set of promising experimental features from various papers