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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
Data Science connector pages
Repositories
32DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
No description provided.
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
No description provided.
Data Science connector pages
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Resources for Connector Instructors
Python and C++ code for reading and writing genomics data.
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JupyterHubs for use by Berkeley enrolled students
Align subreads to ccs reads
Bayesian haplotype-based mutation calling
Patient Genomics Research Case
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"Recurrent Models of Visual Attention" in TensorFlow
ok.py supports programming projects by running tests, tracking progress, and assisting in debugging.
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A convolutional neural network for predicting chromatin accessibility in multiple cell types from DNA sequence
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rllab is a framework for developing and evaluating reinforcement learning algorithms, fully compatible with OpenAI Gym.
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Tutorial materials for deploying JupyterHub
Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.
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Class materials for LS 88-3 Genomics and Data Science
Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.