gagneurlab / dependencies_DNALMLinks
Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements
☆14Updated 5 months ago
Alternatives and similar repositories for dependencies_DNALM
Users that are interested in dependencies_DNALM are comparing it to the libraries listed below
Sorting:
- ☆18Updated last year
- Computational Optimization of DNA Activity (CODA)☆60Updated 5 months ago
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆35Updated 5 months ago
- ☆40Updated last month
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆71Updated 2 months ago
- Saluki, a method to predict mRNA half-lives from sequence☆25Updated 2 years ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆47Updated 10 months ago
- Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"☆22Updated last year
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆44Updated 9 months ago
- ☆33Updated 2 years ago
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆20Updated last year
- ☆23Updated 6 months ago
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.☆31Updated 3 weeks ago
- ☆17Updated 10 months ago
- ☆18Updated last year
- ☆24Updated last year
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆39Updated 2 months ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆66Updated 2 years ago
- HLA-II ligand predictor.☆44Updated 2 years ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 7 months ago
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆19Updated 2 weeks ago
- ☆24Updated last year
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆85Updated last week
- APA Regression Net - Predict and Engineer Alternative Polyadenylation☆39Updated 3 years ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Updated 5 months ago
- ☆72Updated 2 months ago
- Knowledge-primed neural networks☆38Updated 2 years ago
- a framework for predicting global protein-protein interaction networks from dynamic mass spec data☆24Updated last year
- This repository hosts a minimal version of a Python API for BPNet.☆48Updated this week
- Elucidating the Utility of Genomic Elements with Neural Nets☆70Updated 9 months ago