jdiez

mpld3

An interactive data visualization tool which brings matplotlib graphics to the browser using D3.

pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

pbcore

A Python library for reading and writing PacBio® data files

ensembl-variation

The Ensembl Variation Perl API and SQL schema

pip-tools

A set of tools to keep your pinned Python dependencies fresh.

onboarding

Getting started in the yeolab

clinical-filter

filtering trio-based genetic variants in VCFs for clinical review

bsub

python wrapper to submit jobs to bsub (and later qsub)

lsf-python-api

Location for the LSF Python wrapper for controlling all things LSF

python-lsf

Improved interface for the LSF batch job scheduler

denovogear

A program to detect denovo-variants using next-generation sequencing data.

ucd-biocore-galaxy

MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

gff3-pltools

A fast parallel GFF3 parser

gffutils

GFF and GTF file manipulation and interconversion

loftee

callability

Comparison of callability in whole genomes vs. whole exoms

celery-pipelines

Pipelines for Celery

awesome-python

An opinionated list of awesome Python frameworks, libraries, software and resources.

illumiprocessor

pre-process illumina reads

adam

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

scalacheck

Property-based testing for Scala

cell

actor framework for Kombu

scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

Genoverse

HTML5 scrollable genome browser

cloneHD

High-definition reconstruction of clonal composition from next-generation sequencing data

Will_it_Python

Translating R Data Analyses to Python

2014-handy-dist-computing

joblib

Computing with Python functions.

drill

Apache Drill is a distributed MPP query layer for self describing data