ni-lab / personalized-expression-benchmarkLinks
Evaluating genomic sequence models for explaining personalized expression variation
☆19Updated 2 years ago
Alternatives and similar repositories for personalized-expression-benchmark
Users that are interested in personalized-expression-benchmark are comparing it to the libraries listed below
Sorting:
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆44Updated 3 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆89Updated last month
- PyTorch implementation of Basenji2.☆19Updated 8 months ago
- For fine-tuning Enformer using paired WGS & gene expression data☆23Updated 4 months ago
- Computational Optimization of DNA Activity (CODA)☆66Updated 8 months ago
- deep learning-inspired explainable sequence model for transcription initiation☆100Updated 9 months ago
- RNA-seq prediction with deep convolutional neural networks.☆216Updated 4 months ago
- ☆25Updated last year
- ☆42Updated 5 months ago
- ☆25Updated 2 years ago
- ☆34Updated 11 months ago
- code to run sei and obtain sei and sequence class predictions☆109Updated 3 years ago
- Machine learning methods for DNA sequence analysis.☆57Updated 4 months ago
- ☆14Updated last month
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆86Updated 3 months ago
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆92Updated 9 months ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆82Updated last year
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆58Updated this week
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆100Updated 3 months ago
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆24Updated last year
- This repository hosts a minimal version of a Python API for BPNet.☆53Updated 2 months ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆71Updated 2 years ago
- Models and datasets for perturbational single-cell omics☆171Updated 3 years ago
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆38Updated 9 months ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆50Updated last year
- Biological sequence analysis for the modern age.☆258Updated 2 weeks ago
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆196Updated 3 months ago
- Toolset for training quantitative sequence to function models.