arkal
Immuno-Informatician foraying into the Synthetic Lethality space. Arduino/Raspi tinker in my free time.
IDEAYA BiosciencesSan Francisco, CA
Pinned Repositories
bioinfo_tool_wrappers
General Python Wrappers for bioinformatics needs.
bioio
Lightweight C++ library for reading FASTA and FASTQ files.
cgcloud
Image and VM management for Jenkins, Spark and Mesos clusters in EC2
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
rankboost
The scripts that conduct the rank boosting step in the precision immuno pipeline
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
protect
s3am
A fast, parallel, streaming multipart uploader for S3
toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
arkal's Repositories
arkal/bioinfo_tool_wrappers
General Python Wrappers for bioinformatics needs.
arkal/dockernator
This project contains my Dockerfiles for the tool used in the pimmuno project
arkal/one_off_scripts
A repository for example scripts or one-offs that don't belong anywhere else
arkal/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
arkal/bioio
Lightweight C++ library for reading FASTA and FASTQ files.
arkal/cgcloud
Image and VM management for Jenkins, Spark and Mesos clusters in EC2
arkal/rankboost
The scripts that conduct the rank boosting step in the precision immuno pipeline
arkal/CITE-seq-Count
A tool that allows to get UMI counts from a single cell protein assay
arkal/metis
Metis is a file service for Etna applications.
arkal/mutilate
This repository contains all the code for the mutilate project
arkal/noob_life_tips
Just a bunch of random (possibly hacky) scripts that make computing life easier
arkal/PARC
arkal/s3am
A fast, parallel, streaming multipart uploader for S3
arkal/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.
arkal/toil_docker_wrappers
arkal/TransGene_supplementary
The supplementary scripts used in the TransGene Paper
arkal/UCSC_VIPER
The UCSC version of the VIPER package for bioinformatics and systems biology
arkal/UPReview