d-laub / basenji2-pytorch
PyTorch implementation of Basenji2.
☆15Updated last year
Alternatives and similar repositories for basenji2-pytorch:
Users that are interested in basenji2-pytorch are comparing it to the libraries listed below
- Evaluating genomic sequence models for explaining personalized expression variation☆19Updated last year
- ☆26Updated 3 weeks ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆38Updated last month
- Computational Optimization of DNA Activity (CODA)☆55Updated last month
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆57Updated last year
- ☆17Updated 4 months ago
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆35Updated 3 months ago
- code to run sei and obtain sei and sequence class predictions☆97Updated 2 years ago
- deep learning-inspired explainable sequence model for transcription initiation☆93Updated 3 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆67Updated last week
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆70Updated 7 months ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆47Updated this week
- Dataloader for applying sequence models to personalized genomics☆22Updated this week
- RNA-seq prediction with deep convolutional neural networks.☆122Updated 2 months ago
- ☆27Updated last month
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆85Updated 4 months ago
- a toolset for mining multi-dimensional features of the translatome with ribosome profiling data☆16Updated last month
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆140Updated 2 weeks ago
- Elucidating the Utility of Genomic Elements with Neural Nets☆65Updated 2 months ago
- ☆20Updated last year
- This repository hosts a minimal version of a Python API for BPNet.☆36Updated last week
- Notes on single-cell Hi-C technologies, tools, and data☆76Updated 4 months ago
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆82Updated this week
- Codebase for the domain adaptation (cross-species TF binding prediction) project.☆12Updated 2 years ago
- For fine-tuning Enformer using paired WGS & gene expression data☆11Updated 3 weeks ago
- Predicting gene expression levels from genomic sequences☆51Updated 4 years ago
- ☆18Updated 6 months ago
- Bioinformatic tool for Splice site Strength Estimation using RNA-seq☆14Updated 2 years ago
- Saluki, a method to predict mRNA half-lives from sequence☆22Updated 2 years ago
- Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets☆36Updated 10 months ago