jzhoulab / puffinLinks
deep learning-inspired explainable sequence model for transcription initiation
☆97Updated 6 months ago
Alternatives and similar repositories for puffin
Users that are interested in puffin are comparing it to the libraries listed below
Sorting:
- code to run sei and obtain sei and sequence class predictions☆109Updated 2 years ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆78Updated last year
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆84Updated 2 weeks ago
- ☆32Updated 7 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆72Updated this week
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆44Updated 9 months ago
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆177Updated last month
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆91Updated 6 months ago
- Computational Optimization of DNA Activity (CODA)☆60Updated 5 months ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆67Updated 2 years ago
- Biological sequence analysis for the modern age.☆248Updated this week
- This repository hosts a minimal version of a Python API for BPNet.☆49Updated 2 weeks ago
- RNA-seq prediction with deep convolutional neural networks.☆197Updated 2 weeks ago
- PyTorch implementation of Basenji2.☆16Updated 4 months ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Updated 5 months ago
- Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them☆163Updated last year
- ☆75Updated 2 months ago
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Updated 10 months ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆88Updated 11 months ago
- A tool for visualising kmers in 2D space.☆10Updated 6 months ago
- A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence☆33Updated last year
- Machine learning methods for DNA sequence analysis.☆54Updated 2 weeks ago
- ☆24Updated last year
- ☆41Updated last month
- predicting expression effects of human genome variants ab initio from sequence☆132Updated 7 months ago
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆98Updated this week
- a toolset for mining multi-dimensional features of the translatome with ribosome profiling data☆18Updated last month
- A modular framework for multimodal cross-cell-type transcriptional regulation models☆87Updated last month
- For fine-tuning Enformer using paired WGS & gene expression data☆22Updated 2 weeks ago
- ☆17Updated 10 months ago