Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
☆181Mar 19, 2026Updated 3 months ago
Alternatives and similar repositories for bpnet
Users that are interested in bpnet are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- TF MOtif Discovery from Importance SCOres☆185May 13, 2026Updated last month
- BPNet manuscript code.☆12Dec 1, 2020Updated 5 years ago
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆238Jun 9, 2026Updated 3 weeks ago
- Code for reproducing the Sei manuscript results☆17Jan 25, 2022Updated 4 years ago
- Prediction of Active Enhancers and Promoters in a Cell type specific manner using shape matching of histone and/or DNase-I hypersensitivi…☆19Sep 19, 2018Updated 7 years 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.
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆92Sep 24, 2025Updated 9 months ago
- ☆27Apr 15, 2025Updated last year
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆75Apr 28, 2023Updated 3 years ago
- Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal☆250Jun 9, 2026Updated 3 weeks ago
- code to run sei and obtain sei and sequence class predictions☆115Dec 20, 2022Updated 3 years ago
- deep learning-inspired explainable sequence model for transcription initiation☆105Mar 3, 2025Updated last year
- ☆19Mar 24, 2023Updated 3 years ago
- Sequential regulatory activity predictions with deep convolutional neural networks.☆472Jan 15, 2026Updated 5 months ago
- Standard set of data-loaders for training and making predictions for DNA sequence-based models.☆84Sep 3, 2024Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…☆129Jun 19, 2026Updated 2 weeks ago
- The ChIP-Seq peak calling algorithm using convolution neural networks☆15Jan 18, 2021Updated 5 years ago
- ☆27May 29, 2023Updated 3 years ago
- A supervised learning model based on Graph Neural Network to predict gene co-expression from chromatin contacts☆12Mar 22, 2023Updated 3 years ago
- This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'☆96Jul 11, 2023Updated 2 years ago
- Modeling Spatio-temporal Dynamics of Chromatin Marks☆12Aug 2, 2021Updated 4 years ago
- A python extension for quick access to bigWig and bigBed files☆245Jan 14, 2026Updated 5 months ago
- Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)☆261Mar 24, 2026Updated 3 months ago
- Toolset for training quantitative sequence to function models.☆23Mar 15, 2024Updated 2 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Elucidating the Utility of Genomic Elements with Neural Nets☆69Dec 2, 2024Updated last year
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆102Mar 1, 2025Updated last year
- Convolutional neural network analysis for predicting DNA sequence activity.☆267Sep 14, 2020Updated 5 years ago
- a framework for training sequence-level deep learning networks☆403Dec 16, 2024Updated last year
- Detecting sites of genomic enrichment☆201May 8, 2023Updated 3 years ago
- Machine learning methods for DNA sequence analysis.☆63Jun 10, 2026Updated 3 weeks ago
- RNA-seq prediction with deep convolutional neural networks.☆248Aug 28, 2025Updated 10 months ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆83Jan 24, 2025Updated last year
- Performant Pythonic GenomicRanges☆494Apr 23, 2026Updated 2 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Evaluating genomic sequence models for explaining personalized expression variation☆20Dec 6, 2023Updated 2 years ago
- ☆19Mar 21, 2024Updated 2 years ago
- Foundation Models for Genomics & Transcriptomics☆890Feb 24, 2026Updated 4 months ago
- Jupyter notebook based genomic data visualization toolkit.☆257Jun 8, 2026Updated 3 weeks ago
- Extract 3D contacts (.pairs) from sequencing alignments☆133Feb 3, 2026Updated 5 months ago
- python module to plot beautiful and highly customizable genome browser tracks☆889Jul 10, 2024Updated last year
- General Use Scripts and Helper functions☆16Mar 29, 2018Updated 8 years ago