Toolkit for single-cell DNA methylation analysis.
☆47Mar 16, 2026Updated last month
Alternatives and similar repositories for ALLCools
Users that are interested in ALLCools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Mapping pipeline for snmC-seq based technologies.☆20Sep 25, 2023Updated 2 years ago
- ☆73Nov 21, 2025Updated 5 months ago
- A spatial genome aligner for analyzing multiplexed DNA-FISH imaging data.☆18Oct 10, 2023Updated 2 years ago
- SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data☆42Jul 6, 2023Updated 2 years ago
- ☆13Mar 29, 2024Updated 2 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆20Sep 12, 2023Updated 2 years ago
- Code and data sharing of Liu et al. 2023 manuscript☆17Apr 18, 2023Updated 3 years ago
- Gene regulatory network inference for RNA velocity and pseudotime data☆29Nov 6, 2025Updated 5 months ago
- ☆27Apr 15, 2025Updated last year
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆92Oct 29, 2025Updated 6 months ago
- ☆55Aug 1, 2024Updated last year
- Code used to analyze single cell RNA and ATAC sequencing in developing human brain☆36Jan 4, 2022Updated 4 years ago
- Nextflow implementation of SpliZ☆15Aug 21, 2023Updated 2 years ago
- MERFISH decoding software☆26Aug 16, 2025Updated 8 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.
- Modelling DNA methylation profiles☆24Jul 16, 2020Updated 5 years ago
- ☆18Mar 31, 2026Updated 3 weeks ago
- Information-based dimensionality reduction☆29Dec 14, 2024Updated last year
- ☆10Dec 11, 2024Updated last year
- Enhancing spatial transcriptomics data by predicting the expression of unmeasured genes from a dissociated scRNA-seq data☆41Jul 1, 2024Updated last year
- ☆12Aug 6, 2025Updated 8 months ago
- ☆38Sep 5, 2024Updated last year
- Toolbox of the Human Neural Organoid Cell Atlas☆33Updated this week
- R package for gene selection using k-NN graphs.☆13Jun 12, 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.
- ☆13Sep 4, 2025Updated 7 months ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).☆58Oct 8, 2021Updated 4 years ago
- Code for scKINETICS (ISMB 2023)☆22Oct 23, 2023Updated 2 years ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆78Nov 13, 2025Updated 5 months ago
- ☆19Mar 19, 2026Updated last month
- ☆12Nov 9, 2020Updated 5 years ago
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated 9 months ago
- scPrisma is a spectral analysis method, for pseudotime reconstruction, informative genes inference, filtering, and enhancement of underly…☆19Mar 31, 2024Updated 2 years 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.
- Python package with CLI for the analysis of single cell methylation data. Now known as MethSCAn: https://github.com/anders-biostat/MethSC…☆12Mar 22, 2024Updated 2 years ago
- SingleCellFusion--a tool to integrate single-cell transcriptome and epigenome data☆12Mar 13, 2022Updated 4 years ago
- ☆13Jun 6, 2024Updated last year
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆41Jan 11, 2025Updated last year
- ☆13Nov 3, 2023Updated 2 years ago
- Single-cell Case Control Analysis☆56Feb 26, 2026Updated 2 months ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆118Oct 31, 2025Updated 6 months ago