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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.

align-clr-to-ccs

Align subreads to ccs reads

bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.

cannoli

Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.

connector-sites

course-repo-example

course-repo-template

datahub

JupyterHubs for use by Berkeley enrolled students

decal-lab

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

distributed_pytorch

easy-course-webpage

genomics-datascience

Class materials for LS 88-3 Genomics and Data Science

gunjanbaid.github.io

hg002-ccs

jupyter-widgets-demo

jupyterhub-tutorial

Tutorial materials for deploying JupyterHub

markdown-site-template

nucleus

Python and C++ code for reading and writing genomics data.

octopus

Bayesian haplotype-based mutation calling

ok

ok.py supports programming projects by running tests, tracking progress, and assisting in debugging.

orbweaver

A convolutional neural network for predicting chromatin accessibility in multiple cell types from DNA sequence

ram

"Recurrent Models of Visual Attention" in TensorFlow

rllab

rllab is a framework for developing and evaluating reinforcement learning algorithms, fully compatible with OpenAI Gym.

test-ga

test-site

trapes

TCR Reconstruction Algorithm for Paired-End Single cell

undiagnosed-1

Patient Genomics Research Case

url-to-interact