Lotfollahi-lab / nichecompass-reproducibilityView external linksLinks
Reproducible analyses for the NicheCompass manuscript
☆13Jul 3, 2025Updated 7 months ago
Alternatives and similar repositories for nichecompass-reproducibility
Users that are interested in nichecompass-reproducibility are comparing it to the libraries listed below
Sorting:
- ☆13Nov 3, 2023Updated 2 years ago
- End-to-end analysis of spatial multi-omics data☆102Jan 26, 2026Updated 3 weeks ago
- R package for normalisation of spatial transcriptomics data☆17Jan 21, 2026Updated 3 weeks ago
- R package for gene selection using k-NN graphs.☆13Jun 12, 2023Updated 2 years ago
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆24Apr 8, 2025Updated 10 months ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆73Nov 13, 2025Updated 3 months ago
- ☆13Aug 9, 2022Updated 3 years ago
- ☆13Sep 3, 2025Updated 5 months ago
- Trends in single cell papers☆17Sep 23, 2024Updated last year
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆118Updated this week
- An offical repo for paper "Single-cells are Spatial Tokens: Transformers for Spatially Resolved Transcriptomics Data Imputation"☆18Aug 11, 2023Updated 2 years ago
- Spatial reconstruction of dissociated single-cell data☆19Jan 12, 2024Updated 2 years ago
- Unsupervised Deep Disentangled Representation of Single-Cell Omics☆60Updated this week
- ☆17Mar 18, 2025Updated 10 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 …☆21Feb 14, 2023Updated 3 years ago
- De novo reconstruction of cell interaction landscapes from single-cell spatial transcriptome data☆21Oct 11, 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…☆29Aug 20, 2025Updated 5 months ago
- ☆22Jan 6, 2026Updated last month
- CellNavi is a deep learning framework designed to predict genes driving cellular transitions.☆45Mar 4, 2025Updated 11 months ago
- conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics☆29Feb 16, 2024Updated 2 years ago
- Information-based dimensionality reduction☆29Dec 14, 2024Updated last year
- Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics (STAGATE software based on pyG framewo…☆62Nov 10, 2023Updated 2 years ago
- Bayesian model for RNA velocity estimation of periodic manifolds☆34Jun 25, 2024Updated last year
- Analysis of imbalanced data and its impacts in a scRNA-seq integration setting☆31Mar 7, 2025Updated 11 months ago
- Repository for Nicheformer: a foundation model for single-cell and spatial omics☆151Nov 23, 2025Updated 2 months ago
- The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains☆34Apr 11, 2025Updated 10 months ago
- Read, modify and write DICOS files with python code☆12Nov 24, 2025Updated 2 months ago
- Ambrogio is a dev agent who tackles tech debt. Starting with automatic unit tests and docstring.☆14Mar 30, 2025Updated 10 months ago
- A single-cell analysis toolkit to jointly analyze samples from distinct conditions☆34Apr 2, 2025Updated 10 months ago
- Bayesian Analytics for Spatial Segmentation☆30May 4, 2025Updated 9 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆150Jan 19, 2026Updated 3 weeks ago
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆78Jul 25, 2025Updated 6 months ago
- ☆33Jan 23, 2025Updated last year
- Cellsnake tool main repo☆36Feb 22, 2024Updated last year
- Weakly supervised learning uncovers phenotypic signatures in single-cell data☆38Dec 17, 2025Updated last month
- ☆10Dec 4, 2023Updated 2 years ago
- Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data☆41Nov 18, 2021Updated 4 years ago
- scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled cluster…☆37Jul 24, 2023Updated 2 years ago
- Dependency-aware deep generative models for multitasking analysis of spatial genomics data☆41Jul 10, 2024Updated last year