Reproducible analyses for the NicheCompass manuscript
☆14Jul 3, 2025Updated 11 months ago
Alternatives and similar repositories for nichecompass-reproducibility
Users that are interested in nichecompass-reproducibility are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆13Nov 3, 2023Updated 2 years ago
- End-to-end analysis of spatial multi-omics data☆116May 15, 2026Updated last month
- De novo reconstruction of cell interaction landscapes from single-cell spatial transcriptome data☆21Oct 11, 2022Updated 3 years ago
- R package for gene selection using k-NN graphs.☆14Jun 12, 2023Updated 3 years ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆82Nov 13, 2025Updated 7 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.
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆25Apr 8, 2025Updated last year
- R package for normalisation of spatial transcriptomics data☆18Jan 21, 2026Updated 4 months ago
- ☆17Mar 18, 2025Updated last year
- Simple ftrl implementation in R for the AVAZU CTR Competition in R☆13Jan 21, 2015Updated 11 years ago
- ☆16May 13, 2022Updated 4 years ago
- Trends in single cell papers☆17Sep 23, 2024Updated last year
- ☆12Dec 6, 2023Updated 2 years ago
- Spatial reconstruction of dissociated single-cell data☆20Jan 12, 2024Updated 2 years ago
- ☆13Aug 9, 2022Updated 3 years ago
- 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.
- ☆13Sep 3, 2025Updated 9 months ago
- An offical repo for paper "Single-cells are Spatial Tokens: Transformers for Spatially Resolved Transcriptomics Data Imputation"☆18Aug 11, 2023Updated 2 years ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆130Updated this week
- conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics☆29Feb 16, 2024Updated 2 years ago
- This is the repository for SeCNV, a single cell copy number profiling tool.☆12Dec 12, 2024Updated last year
- Reproduce analyses and baselines from the State paper☆15Feb 25, 2026Updated 3 months ago
- Framework for Unified Single-Cell Analysis (FUSCA) is a software package for single-cell data analysis developed in R. At the moment, it …☆22Feb 14, 2023Updated 3 years ago
- Unsupervised Deep Disentangled Representation of Single-Cell Omics☆70Updated this week
- NeST-VNN repo☆12Jun 13, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Code for spatial subclone paper☆18Jan 23, 2025Updated last year
- ☆10Dec 4, 2024Updated last year
- ☆10Nov 29, 2022Updated 3 years ago
- scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (e…☆32Aug 20, 2025Updated 9 months ago
- Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics (STAGATE software based on pyG framewo…☆69Nov 10, 2023Updated 2 years ago
- A computational tool for identification of 3D multi-modal spatial neighborhoods☆15Aug 1, 2025Updated 10 months ago
- Information-based dimensionality reduction☆30Dec 14, 2024Updated last year
- ☆15Dec 30, 2024Updated last year
- The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains☆34Apr 11, 2025Updated last year
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆176May 25, 2026Updated 3 weeks ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆100Dec 11, 2023Updated 2 years ago
- ☆23Jan 6, 2026Updated 5 months ago
- [MICCAI'25] LesionDiffusion, a general, text-controllable lesion synthesis foundation model for 3D CT imaging.☆20Jan 19, 2026Updated 5 months ago
- ☆14Dec 11, 2023Updated 2 years ago
- A comprehensive tool to infer TF-centred, spatial gene regulatory networks for the spatially resolved transcriptomic data.☆22Apr 27, 2025Updated last year
- Official Implementation of Avoiding spurious correlations via logit correction☆17May 6, 2023Updated 3 years ago