Top 6 Jupyter Notebook Genomic Projects

DNA-Diffusion

4 334 8.3 Jupyter Notebook

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
HLA

2 94 0.0 Jupyter Notebook

xHLA: Fast and accurate HLA typing from short read sequence data

Project mention: HLA-Genotyping | /r/Nebulagenomics | 2023-05-19

xHLA on GitHub worked for me running it directly on the Nebula cram file with no additional processing. Results match those from OptiType (which had high memory requirements, was much slower and only covered 3 of the 6 common genes).

InfluxDB

www.influxdata.com sponsored

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
full_spectrum_bioinformatics

1 67 6.2 Jupyter Notebook

An open-access bioinformatics text
ezancestry

1 55 7.7 Jupyter Notebook

Easy genetic ancestry predictions in Python
synthetic-data-genomics

3 32 0.0 Jupyter Notebook

Proof of concept code from Gretel.ai and Illumina using generative neural networks to create synthetic versions of mouse genotype and phenotype data.
amazon-genomics-cli-demos

1 3 0.0 Jupyter Notebook

Demos of what can be done with the Amazon Genomics CLI

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).