Reproducible Snakemake workflow for benchmarking single-cell chromatin accessibility analysis methods, published in https://doi.org/10.1186/s13059-024-03356-x
☆17Jan 24, 2026Updated 3 months ago
Alternatives and similar repositories for sc_chromatin_benchmark
Users that are interested in sc_chromatin_benchmark are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Supplementary files and notebooks to recreate figures.☆21Aug 12, 2025Updated 8 months ago
- Identifying transcription factor binding sites from neural network contribution scores☆18Nov 8, 2025Updated 6 months ago
- Flexible linear mixed model framework for Genome Wide Association Studies☆18Nov 6, 2025Updated 6 months ago
- Parse ArchR arrow files to anndata h5ad☆16Dec 14, 2023Updated 2 years ago
- Code for our paper: https://www.biorxiv.org/content/10.1101/528463v1☆18Apr 24, 2020Updated 6 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Code to reproduce analysis of Milo manuscript☆15Aug 3, 2022Updated 3 years ago
- Original materials for the "Introduction to Solving Biological Problems with Python" 2 days course☆10Jun 25, 2018Updated 7 years ago
- A Julia package for fitting VAEs to single-cell data using count distributions.☆25Feb 16, 2026Updated 2 months ago
- jinja2-enabled jupyter notebooks☆37Feb 13, 2026Updated 2 months ago
- An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)☆39Aug 22, 2024Updated last year
- ☆15Apr 8, 2026Updated last month
- Single-cell epigenomics analysis tools☆317Mar 13, 2026Updated last month
- ☆15Sep 27, 2022Updated 3 years ago
- ☆13Mar 13, 2026Updated last month
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- tools in python and R for analyzing biological count data, especially from single cell RNAseq☆23Feb 1, 2024Updated 2 years ago
- ☆10Sep 20, 2022Updated 3 years ago
- Quantitative Trait Cluster Association Test in R☆26Apr 19, 2021Updated 5 years ago
- scRNA-seq data visualization from scrattch☆30Aug 20, 2025Updated 8 months ago
- Onboarding materials for the Greene Lab☆33Feb 10, 2026Updated 3 months ago
- Notebooks for generating figures in "Progressive Plasticity During Colorectal Cancer Metastasis"☆22Dec 1, 2024Updated last year
- Quick access to gene synonyms☆29Updated this week
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆41Jan 11, 2025Updated last year
- Single Cell Analysis of Five'Ends☆52Mar 19, 2024Updated 2 years 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.
- ☆19Dec 15, 2023Updated 2 years ago
- Repository☆10Oct 23, 2024Updated last year
- a collection of colabs useful for molecular biology☆33Feb 27, 2024Updated 2 years ago
- A module for working with snap files in Python☆37May 5, 2020Updated 6 years ago
- ☆44Apr 15, 2026Updated 3 weeks ago
- pipeline for demultiplex and align both ATAC and RNA data generated in SHARE-seq☆16Jun 20, 2022Updated 3 years ago
- Experimental Marimo extension for Agentic Notebooks -- integrating AI Agents into the Notebook workflow☆15Oct 11, 2025Updated 7 months ago
- ☆10Jan 19, 2019Updated 7 years ago
- Evaluation framework for computationally inferred gene networks from single-cell data.☆18Oct 23, 2025Updated 6 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- CELLama Project☆23Nov 15, 2025Updated 5 months ago
- Explainable Multilayer Graph Neural Network for Cancer Gene Prediction☆21Nov 3, 2023Updated 2 years ago
- ☆19Oct 27, 2021Updated 4 years ago
- ☆55Nov 28, 2025Updated 5 months ago
- CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…☆72May 4, 2026Updated last week
- 3DGB is a workflow to build 3D models of genomes from HiC data☆13Updated this week
- A record of the analysis pipelines used to create the HTAPP data☆34Apr 15, 2025Updated last year