wenduocheng / DNALongBenchLinks
☆15Updated 3 months ago
Alternatives and similar repositories for DNALongBench
Users that are interested in DNALongBench are comparing it to the libraries listed below
Sorting:
- ☆26Updated 2 years ago
- ☆18Updated last year
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆44Updated last week
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆38Updated 10 months ago
- ☆18Updated last year
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆91Updated 2 months ago
- ☆34Updated last year
- deep learning-inspired explainable sequence model for transcription initiation☆100Updated 10 months ago
- ☆22Updated 3 weeks ago
- ☆42Updated this week
- Computational Optimization of DNA Activity (CODA)☆67Updated 9 months ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆50Updated last year
- For fine-tuning Enformer using paired WGS & gene expression data☆26Updated 5 months ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆91Updated 3 months ago
- Repository for the paper: "SPACE: STRING proteins as complementary embeddings"☆33Updated last month
- Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"☆23Updated last year
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Updated last year
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆24Updated last year
- ☆25Updated 4 months ago
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.☆54Updated 2 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆86Updated 4 months ago
- ☆25Updated 5 months ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Updated 9 months ago
- Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…☆120Updated last week
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆82Updated last year
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆22Updated 4 months ago
- NeuronMotif: deciphering cis-regulatory codes by layerwise demixing of deep neural networks☆15Updated 2 years ago
- Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements☆25Updated 10 months ago
- SIMBA: SIngle-cell eMBedding Along with features☆66Updated last year
- scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism☆18Updated last year