1edv / evolutionLinks
This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'
☆95Updated last year
Alternatives and similar repositories for evolution
Users that are interested in evolution are comparing it to the libraries listed below
Sorting:
- Computational Optimization of DNA Activity (CODA)☆59Updated 2 months ago
- ☆74Updated last year
- BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity☆53Updated last year
- Detailed explanation on how to setup database for NCBI IgBlast executable, and using it in Python☆28Updated 2 years ago
- ☆28Updated 4 months ago
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆36Updated last month
- Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them☆154Updated 10 months ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆75Updated 10 months ago
- ☆34Updated last month
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆63Updated 2 years ago
- Modeling of human 5′ UTRs enables the design of new sequences for target levels of translation and 5′ UTR variant prediction.☆47Updated 5 years ago
- code to run sei and obtain sei and sequence class predictions☆105Updated 2 years ago
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆174Updated last year
- Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…☆59Updated last week
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆56Updated 2 weeks ago
- Draw RNA secondary structures in python.☆48Updated 9 months ago
- python tools for TCR:peptide-MHC modeling and analysis☆75Updated last year
- Predicting gene expression levels from genomic sequences☆53Updated 4 years ago
- deep learning-inspired explainable sequence model for transcription initiation☆94Updated 3 months ago
- Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data☆119Updated 2 years ago
- Collection of papers related to BCR repertoire analyses☆18Updated 3 years ago
- immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.☆68Updated last week
- ExplaiNN: interpretable and transparent neural networks for genomics☆48Updated 2 months ago
- Multi-class signal peptide prediction and structure decoding model.☆84Updated 4 months ago
- NetTCR-2.0. Sequence-based prediction of peptide-TCR binding☆34Updated 3 years ago
- HLA-II ligand predictor.☆43Updated 2 years ago
- Evolutionary velocity with protein language models☆90Updated last year
- Package to Score Sequences using Rule Set 3☆11Updated last year
- Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"☆19Updated 11 months ago
- The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)☆35Updated last year