kundajelab / bpnetView external linksLinks
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
☆174Oct 10, 2025Updated 4 months ago
Alternatives and similar repositories for bpnet
Users that are interested in bpnet are comparing it to the libraries listed below
Sorting:
- TF MOtif Discovery from Importance SCOres☆165Dec 14, 2025Updated 2 months ago
- BPNet manuscript code.☆12Dec 1, 2020Updated 5 years ago
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆208Feb 2, 2026Updated last week
- Code for reproducing the Sei manuscript results☆17Jan 25, 2022Updated 4 years ago
- ☆27Apr 15, 2025Updated 9 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆87Sep 24, 2025Updated 4 months ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆72Apr 28, 2023Updated 2 years ago
- This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'☆96Jul 11, 2023Updated 2 years ago
- Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal☆237Dec 2, 2025Updated 2 months ago
- code to run sei and obtain sei and sequence class predictions☆111Dec 20, 2022Updated 3 years ago
- Machine learning methods for DNA sequence analysis.☆57Feb 2, 2026Updated last week
- 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
- Sequential regulatory activity predictions with deep convolutional neural networks.☆462Jan 15, 2026Updated 3 weeks ago
- Toolset for training quantitative sequence to function models.☆23Mar 15, 2024Updated last year
- ☆19Mar 24, 2023Updated 2 years ago
- Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)☆246Jan 31, 2026Updated 2 weeks ago
- deep learning-inspired explainable sequence model for transcription initiation☆100Mar 3, 2025Updated 11 months ago
- A supervised learning model based on Graph Neural Network to predict gene co-expression from chromatin contacts☆12Mar 22, 2023Updated 2 years ago
- Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…☆124Oct 3, 2025Updated 4 months ago
- The ChIP-Seq peak calling algorithm using convolution neural networks☆15Jan 18, 2021Updated 5 years ago
- Extract 3D contacts (.pairs) from sequencing alignments☆125Feb 3, 2026Updated last week
- A python extension for quick access to bigWig and bigBed files☆239Jan 14, 2026Updated last month
- a framework for training sequence-level deep learning networks☆397Dec 16, 2024Updated last year
- Elucidating the Utility of Genomic Elements with Neural Nets☆69Dec 2, 2024Updated last year
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆79Jan 24, 2025Updated last year
- Standard set of data-loaders for training and making predictions for DNA sequence-based models.☆83Sep 3, 2024Updated last year
- Convolutional neural network analysis for predicting DNA sequence activity.☆267Sep 14, 2020Updated 5 years ago
- Integrated Genome Modeling (IGM): multi-modal data-driven simulator of genome structures☆12Jun 15, 2023Updated 2 years ago
- Modeling Spatio-temporal Dynamics of Chromatin Marks☆12Aug 2, 2021Updated 4 years ago
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆95Mar 1, 2025Updated 11 months ago
- General Use Scripts and Helper functions☆16Mar 29, 2018Updated 7 years ago
- Detecting sites of genomic enrichment☆198May 8, 2023Updated 2 years ago
- Performant Pythonic GenomicRanges☆493Jan 27, 2026Updated 2 weeks ago
- A Python package for fast operations on 1-dimensional genomic signal tracks☆23Apr 3, 2020Updated 5 years ago
- ☆27May 29, 2023Updated 2 years ago
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆100Sep 9, 2025Updated 5 months ago
- nanoNOMe (Nucleosome Occupancy and Methylome nanopore sequencing) Analysis☆20Nov 18, 2022Updated 3 years ago
- Base-pair resolution detection of transcription factor binding site by deep deconvolutional network☆10Sep 12, 2017Updated 8 years ago
- RNA-seq prediction with deep convolutional neural networks.☆225Aug 28, 2025Updated 5 months ago