Toolset for training quantitative sequence to function models.
☆23Mar 15, 2024Updated 2 years ago
Alternatives and similar repositories for gopher
Users that are interested in gopher are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics☆25Jun 3, 2025Updated 11 months ago
- ENNGene: an Easy Neural Network model building tool for Genomics☆11Mar 31, 2022Updated 4 years ago
- ☆13Jan 23, 2025Updated last year
- ☆34Jan 27, 2025Updated last year
- A framework to score and analyze variant effects genome-wide using ChromBPNet models☆17Mar 2, 2026Updated 2 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆29Feb 21, 2023Updated 3 years ago
- ☆25Aug 20, 2024Updated last year
- A command-line tool to mitigate homology-based data leakage in sequence-to-expression models☆20Mar 29, 2026Updated last month
- Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) i…☆16Jun 25, 2025Updated 11 months ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆32Jan 22, 2025Updated last year
- ☆12Oct 4, 2021Updated 4 years ago
- A fast dataloader for bigwig files made for machine learning☆29Dec 16, 2025Updated 5 months ago
- A method for analyzing scATAC-seq experiments.☆33Jun 20, 2025Updated 11 months ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆65Updated this week
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Code used to analyze single cell RNA and ATAC sequencing in developing human brain☆36Jan 4, 2022Updated 4 years ago
- Standard set of data-loaders for training and making predictions for DNA sequence-based models.☆83Sep 3, 2024Updated last year
- Machine learning methods for DNA sequence analysis.☆63Feb 27, 2026Updated 2 months ago
- This repository hosts a minimal version of a Python API for BPNet.☆56Jan 24, 2026Updated 4 months ago
- ☆10Dec 11, 2024Updated last year
- ☆19Mar 21, 2024Updated 2 years ago
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆44Jul 3, 2025Updated 10 months ago
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆98Mar 1, 2025Updated last year
- Elucidating the Utility of Genomic Elements with Neural Nets☆69Dec 2, 2024Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Accompanying repository for GkmExplain paper☆23Aug 20, 2020Updated 5 years ago
- Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.☆107Jan 31, 2026Updated 3 months ago
- surrogate quantitative interpretability for deepnets☆24Aug 11, 2025Updated 9 months ago
- ☆11Feb 6, 2023Updated 3 years ago
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆55Jan 19, 2026Updated 4 months ago
- Sequential regulatory activity predictions with deep convolutional neural networks.☆470Jan 15, 2026Updated 4 months ago
- code to run sei and obtain sei and sequence class predictions☆114Dec 20, 2022Updated 3 years ago
- ☆18Updated this week
- Saluki, a method to predict mRNA half-lives from sequence☆27Oct 7, 2022Updated 3 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)☆38Aug 16, 2023Updated 2 years ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆91Sep 24, 2025Updated 8 months ago
- ☆27Apr 15, 2025Updated last year
- Evaluation framework for computationally inferred gene networks from single-cell data.☆18Oct 23, 2025Updated 7 months ago
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆102Sep 9, 2025Updated 8 months ago
- Predicting gene expression levels from genomic sequences☆54Jun 24, 2020Updated 5 years ago
- Beta-Poisson model for single-cell RNA-seq data analyses☆18Feb 8, 2019Updated 7 years ago