calico / baskervilleLinks
Machine learning methods for DNA sequence analysis.
☆55Updated last month
Alternatives and similar repositories for baskerville
Users that are interested in baskerville are comparing it to the libraries listed below
Sorting:
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆75Updated 3 weeks ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆67Updated 2 years ago
- This repository hosts a minimal version of a Python API for BPNet.☆49Updated last month
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆30Updated 8 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆84Updated last week
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆43Updated last week
- ☆32Updated 8 months ago
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆92Updated 7 months ago
- Toolset for training quantitative sequence to function models.☆23Updated last year
- ☆24Updated last year
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Updated 6 months ago
- Saluki, a method to predict mRNA half-lives from sequence☆25Updated 2 years ago
- Dataloader for applying sequence models to personalized genomics☆27Updated last week
- Elucidating the Utility of Genomic Elements with Neural Nets☆70Updated 10 months ago
- deep learning-inspired explainable sequence model for transcription initiation☆96Updated 7 months ago
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆35Updated 6 months ago
- Predicting gene expression levels from genomic sequences☆54Updated 5 years ago
- code to run sei and obtain sei and sequence class predictions☆109Updated 2 years ago
- A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence☆33Updated last year
- Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.☆19Updated 3 weeks ago
- ☆77Updated 3 months ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆47Updated this week
- Computational Optimization of DNA Activity (CODA)☆61Updated 6 months ago
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.☆33Updated last month
- Analyses related to the Borzoi paper.☆19Updated 2 weeks ago
- Code for reproducing the Sei manuscript results☆17Updated 3 years ago
- ☆40Updated 5 years ago
- A method for analyzing scATAC-seq experiments.☆34Updated 3 months ago
- Knowledge-primed neural networks☆38Updated 2 years ago
- CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…☆47Updated last month