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Wellcome Sanger Institute
- Wellcome Genome Campus
- https://www.sanger.ac.uk/group/parts-group/
- @jhepkema
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Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
Agent framework for constructing language model agents and training on constructive tasks.
Gymnasium framework for training language model agents on constructive tasks
Get up and running with Llama 3.3, DeepSeek-R1, Phi-4, Gemma 2, and other large language models.
High accuracy RAG for answering questions from scientific documents with citations
Work in progress transmit from Google Code
Implementation of paper - YOLOv7: Trainable bag-of-freebies sets new state-of-the-art for real-time object detectors
Particle dynamics and simulated annealing for chromosome structure calculation
ORB forcefield models from Orbital Materials
Official repository for the Boltz-1 biomolecular interaction model
A toolkit for QC and visualization of ATAC-seq results.
Interspecies Point Projection - A tool for comparative genomics beyond alignable sequence
Source code for RNA-FrameFlow: SE(3) Flow Matching for 3D RNA Backbone Design
Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).
Software for the visualization of sequence-function relationships
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
👁️ Python library to plot DNA sequence features (e.g. from Genbank files)
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules.
Script to automatically create and run IGV snapshot batchscripts
Aggregate results from bioinformatics analyses across many samples into a single report.
ATAC-seq peak-calling and QC analysis pipeline
A bioinformatics tool for working with modified bases
Chromatin interaction aware gene regulatory modeling with graph attention networks