songlab-cal / gpnView external linksLinks
Genomic Pre-trained Network
☆321Feb 6, 2026Updated last week
Alternatives and similar repositories for gpn
Users that are interested in gpn are comparing it to the libraries listed below
Sorting:
- Foundation Models for Genomics & Transcriptomics☆821Jan 15, 2026Updated last month
- RNA-seq prediction with deep convolutional neural networks.☆225Aug 28, 2025Updated 5 months ago
- Benchmarking DNA Language Models on Biologically Meaningful Tasks☆129Oct 31, 2024Updated last year
- ☆42Updated this week
- gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.☆314Jan 29, 2026Updated 2 weeks ago
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 6 months ago
- [ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome☆459Jan 1, 2026Updated last month
- Benchmarks for classification of genomic sequences☆172Aug 14, 2025Updated 6 months ago
- ☆22Updated this week
- Learning and Aligning Large Protein Families with support of protein language models.☆30Feb 6, 2026Updated last week
- Genomic language model predicts protein co-regulation and function☆86Mar 19, 2025Updated 10 months ago
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆191Mar 16, 2024Updated last year
- Fast and accurate coordinate conversion between assemblies☆118Oct 9, 2025Updated 4 months ago
- DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome☆738Jan 22, 2026Updated 3 weeks ago
- Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics☆25Jun 3, 2025Updated 8 months ago
- deep learning-inspired explainable sequence model for transcription initiation☆100Mar 3, 2025Updated 11 months ago
- ☆15Feb 8, 2026Updated last week
- CPANG19 - Computational PANGenomics (2019)☆12May 7, 2020Updated 5 years ago
- ☆101Apr 22, 2024Updated last year
- Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena☆758Apr 22, 2025Updated 9 months ago
- Species-aware DNA language modeling☆18Jan 25, 2023Updated 3 years ago
- MEMO: MEM-based pangenome indexing for k-mer queries☆20Jun 11, 2024Updated last year
- ☆86Sep 20, 2023Updated 2 years ago
- ☆31Jun 20, 2025Updated 7 months ago
- Biological foundation modeling from molecular to genome scale☆1,477Nov 19, 2025Updated 2 months ago
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 2 months ago
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆148Jan 27, 2025Updated last year
- Suite of heritability and genetic correlation estimation tools for exome-sequencing data☆35Dec 5, 2025Updated 2 months ago
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆36May 14, 2025Updated 9 months ago
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- Alignment-free genotyper for SNPs and short indels, implemented in Python.☆54Mar 7, 2025Updated 11 months ago
- Efficient low-divergence mapping of long reads in minimizer space☆70Oct 7, 2023Updated 2 years ago
- LongcallR is a SNP caller for single molecule long-read RNA-seq data☆72Dec 14, 2025Updated 2 months ago
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆67Sep 13, 2022Updated 3 years ago
- Constructing a pangenome gene graph☆204Aug 11, 2025Updated 6 months ago
- Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch☆557Jul 7, 2025Updated 7 months ago
- Kmer Analysis of Pileups for Genotyping☆35Jan 30, 2026Updated 2 weeks ago
- ☆79Updated this week
- code to run sei and obtain sei and sequence class predictions☆111Dec 20, 2022Updated 3 years ago