calico / baskervilleLinks
Machine learning methods for DNA sequence analysis.
☆51Updated 3 weeks ago
Alternatives and similar repositories for baskerville
Users that are interested in baskerville are comparing it to the libraries listed below
Sorting:
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆64Updated 2 years ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆68Updated last month
- Toolset for training quantitative sequence to function models.☆23Updated last year
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆44Updated 8 months ago
- This repository hosts a minimal version of a Python API for BPNet.☆47Updated 3 weeks ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 6 months ago
- Elucidating the Utility of Genomic Elements with Neural Nets☆70Updated 8 months ago
- For fine-tuning Enformer using paired WGS & gene expression data☆19Updated 2 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆83Updated last month
- CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…☆43Updated this week
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Updated 4 months ago
- ☆23Updated 11 months ago
- Saluki, a method to predict mRNA half-lives from sequence☆25Updated 2 years ago
- deep learning-inspired explainable sequence model for transcription initiation☆97Updated 5 months ago
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆89Updated 5 months ago
- code to run sei and obtain sei and sequence class predictions☆106Updated 2 years ago
- Predicting gene expression levels from genomic sequences☆53Updated 5 years ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆42Updated last week
- ☆31Updated 6 months ago
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Updated 8 months ago
- A method for analyzing scATAC-seq experiments.☆33Updated last month
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆34Updated 4 months ago
- Dataloader for applying sequence models to personalized genomics☆27Updated last week
- ☆65Updated last month
- Code for reproducing the Sei manuscript results☆17Updated 3 years ago
- Analyses related to the Borzoi paper.☆16Updated last month
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆77Updated last year
- Annotated sequence data☆11Updated 6 months ago
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.☆27Updated this week
- High-definition modeling of chromatin + transcriptomics data☆24Updated 3 months ago