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Top 23 Python Genomic Projects
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deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
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nucleotide-transformer
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
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enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
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hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
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enrich_omics
A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)
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edgecase
A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.
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pestalotiopsis
Assembly and phylogentic analysis pipeline for draft genome of a Pestalotiopsis fungi.
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Maybe it would help you to look at the galaxy project: GitHub main site
Project mention: ResearchAgent: Iterative Research Idea Generation Using LLMs | news.ycombinator.com | 2024-04-20
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).
Python Genomics related posts
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Invitación a proyecto - Biopython en Español
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Snakemake – A framework for reproducible data analysis
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Biopython – Python Tools for Computational Molecular Biology
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comparing the similarity between a set of protein sequences
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Look over my purchase, is there anything I should return?
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u/Responsible-Gas3852 comments on "Why is Cancer so Hard to Cure?"
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My boss is considering letting me take a programming course if I have some good reasons why.
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A note from our sponsor - SaaSHub
www.saashub.com | 2 Jun 2024
Index
What are some of the best open-source Genomic projects in Python? This list will help you:
| Project | Stars | |
|---|---|---|
| 1 | Biopython | 4,203 |
| 2 | deepvariant | 3,098 |
| 3 | galaxy | 1,326 |
| 4 | Hail | 944 |
| 5 | ncbi-genome-download | 898 |
| 6 | goatools | 734 |
| 7 | pyCirclize | 642 |
| 8 | eggnog-mapper | 538 |
| 9 | pyfaidx | 442 |
| 10 | nucleotide-transformer | 405 |
| 11 | enformer-pytorch | 399 |
| 12 | truvari | 296 |
| 13 | hgvs | 232 |
| 14 | pyGenomeViz | 237 |
| 15 | ariba | 155 |
| 16 | Scoary | 137 |
| 17 | covid-19-genomes | 45 |
| 18 | UPIMAPI | 26 |
| 19 | arcsv | 21 |
| 20 | enrich_omics | 17 |
| 21 | edgecase | 14 |
| 22 | biology | 13 |
| 23 | pestalotiopsis | 7 |
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