CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
☆81Sep 22, 2026Updated this week
Alternatives and similar repositories for CREsted
Users that are interested in CREsted are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Transcription Factor Motif Instance Neighborhood Decomposition and Interpretation☆26Sep 11, 2026Updated last week
- Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.☆22Updated this week
- ☆29Dec 10, 2025Updated 9 months ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆85Sep 15, 2026Updated last week
- Identifying transcription factor binding sites from neural network contribution scores☆26Aug 26, 2026Updated 3 weeks ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Open4Gene, A Hurdle Model-based Method for Peak-to-Gene Linkage Analysis☆18Mar 17, 2026Updated 6 months ago
- A framework to score and analyze variant effects genome-wide using ChromBPNet models☆21Mar 2, 2026Updated 6 months ago
- ☆79May 27, 2026Updated 3 months ago
- Biological sequence analysis for the modern age.☆311Updated this week
- Code & documentation for Multiomics and deep learning dissect regulatory syntax in human development (Liu*, Jessa*, Kim*, Ng*, et al, Nat…☆32Jul 17, 2026Updated 2 months ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆264Jan 16, 2026Updated 8 months ago
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆253Jun 9, 2026Updated 3 months ago
- pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence …☆21Apr 14, 2026Updated 5 months ago
- SCENIC+ analyses☆18Sep 26, 2023Updated 2 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- ☆13Jan 23, 2025Updated last year
- Deep learning models to predict enhancers in different Drosophila embryo tissues☆20Dec 10, 2023Updated 2 years ago
- ☆12Oct 4, 2021Updated 4 years ago
- systematic explanation of attribution-based mechanisms for regulatory genomics☆18Sep 16, 2026Updated last week
- ☆51Updated this week
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆40Mar 27, 2025Updated last year
- Machine learning methods for DNA sequence analysis.☆66Updated this week
- High-definition modeling of chromatin + transcriptomics data☆26Jan 27, 2026Updated 7 months ago
- Consensus peaks of chromatin accessibility in the human genome☆18Dec 1, 2025Updated 9 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- RNA-seq prediction with deep convolutional neural networks.☆264Updated this week
- This repository hosts a minimal version of a Python API for BPNet.☆60Jul 19, 2026Updated 2 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆99Jun 10, 2026Updated 3 months ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆32Jan 22, 2025Updated last year
- PARM: Promoter Activity Regulatory Model☆26Jul 27, 2026Updated last month
- A repository of pipelines for single-cell data in Nextflow DSL2☆81Apr 19, 2023Updated 3 years ago
- Computational Optimization of DNA Activity (CODA)☆68Apr 3, 2025Updated last year
- GAME was designed for the functional genomics community to create seamless communication across pre-trained models and genomics datasets.…☆23Aug 26, 2026Updated 3 weeks ago
- AlphaGenome PyTorch port☆161Sep 15, 2026Updated last week
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- A method for analyzing scATAC-seq experiments.☆33Jun 20, 2025Updated last year
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆76Apr 28, 2023Updated 3 years ago
- R and MATLAB scripts for MAGICAL☆12Jun 26, 2024Updated 2 years ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆84Jun 4, 2026Updated 3 months ago
- Reproducible Snakemake workflow for benchmarking single-cell chromatin accessibility analysis methods, published in https://doi.org/10.11…☆17Jan 24, 2026Updated 7 months ago
- GIANT (Gene-based data Integration and ANalysis Technique) is a method for large-scale joint analyses of atlas-level single cell data.☆14Jun 13, 2023Updated 3 years ago
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆16Oct 16, 2025Updated 11 months ago