arkal

bioinfo_tool_wrappers

General Python Wrappers for bioinformatics needs.

dockernator

This project contains my Dockerfiles for the tool used in the pimmuno project

one_off_scripts

A repository for example scripts or one-offs that don't belong anywhere else

Transgene

This is a repository to host the transgene tool. Transgene takes a snpeffed vcf and a peptide fasta , and returns 3 peptide fastas containing 9-, 10- and 15-mers harboring the called mutations

bioio

Lightweight C++ library for reading FASTA and FASTQ files.

cgcloud

Image and VM management for Jenkins, Spark and Mesos clusters in EC2

rankboost

The scripts that conduct the rank boosting step in the precision immuno pipeline

CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay

metis

Metis is a file service for Etna applications.

mutilate

This repository contains all the code for the mutilate project

noob_life_tips

Just a bunch of random (possibly hacky) scripts that make computing life easier

PARC

s3am

A fast, parallel, streaming multipart uploader for S3

toil

Python based pipeline management software for clusters that makes running recursive and dynamically scheduled computations straightforward. So far works with gridEngine, lsf, parasol and on multi-core machines.

toil_docker_wrappers

TransGene_supplementary

The supplementary scripts used in the TransGene Paper

UCSC_VIPER

The UCSC version of the VIPER package for bioinformatics and systems biology

UPReview