Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
☆46Aug 18, 2025Updated 6 months ago
Alternatives and similar repositories for CalicoST
Users that are interested in CalicoST are comparing it to the libraries listed below
Sorting:
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆30Jul 22, 2024Updated last year
- Hotspot cluster distance analysis in spatial transcriptomic data☆35Feb 10, 2025Updated last year
- Code for spatial subclone paper☆16Jan 23, 2025Updated last year
- A set of Pyro models and functions to infer CNA from scRNA-seq data☆11Aug 14, 2023Updated 2 years ago
- Construct Tumor Transition Zone Microenvironment☆55Jun 25, 2025Updated 8 months ago
- Notebooks for generating figures in "Progressive Plasticity During Colorectal Cancer Metastasis"☆17Dec 1, 2024Updated last year
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆90Dec 8, 2022Updated 3 years ago
- Draw phylogenetic trees of tumor evolution☆87Jul 21, 2023Updated 2 years ago
- Gene group activity utility functions for Scanpy☆100Dec 21, 2024Updated last year
- ☆271Oct 13, 2025Updated 4 months ago
- Detecting and dissecting anomalous anatomic regions in spatial transcriptomics with STANDS☆11Dec 27, 2024Updated last year
- scMalignantFinder is a Python package specially designed for analyzing cancer single-cell RNA-seq datasets to distinguish malignant cells…☆17Feb 20, 2026Updated last week
- cell type specific, trait-associated gene regulation☆29Mar 31, 2025Updated 11 months ago
- R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data☆35Jan 13, 2026Updated last month
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆152Feb 12, 2026Updated 2 weeks ago
- ☆18Feb 5, 2025Updated last year
- ☆11May 24, 2024Updated last year
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆204Feb 4, 2026Updated 3 weeks ago
- End-to-end analysis of spatial multi-omics data☆104Jan 26, 2026Updated last month
- Morphology-Enhanced Spatial Transcriptome Analysis Integrator☆27Mar 16, 2025Updated 11 months ago
- ☆13Sep 30, 2024Updated last year
- Scanner of specific spatial patterns in tissues☆14Jul 15, 2022Updated 3 years ago
- ☆12Sep 29, 2023Updated 2 years ago
- Publically accessible code for DIISCO method☆12Oct 15, 2025Updated 4 months ago
- GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data☆70Dec 1, 2025Updated 2 months ago
- ☆17Oct 23, 2025Updated 4 months ago
- Cell level integrated analysis of tissue histology and spatial transcriptomics☆31Oct 6, 2025Updated 4 months ago
- Developmental Spatiotemporal Optimal Transport☆13Mar 19, 2025Updated 11 months ago
- Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper☆27Nov 21, 2022Updated 3 years ago
- Learning notes for DBiT-Notes☆11Nov 28, 2024Updated last year
- Spatial omics analysis toolbox☆362Feb 12, 2026Updated 2 weeks ago
- ☆13Aug 9, 2022Updated 3 years ago
- SenePy is a set of tools to score single-cells based on their expression of cell-specific senescence markers. Please see the following pu…☆50Jan 30, 2025Updated last year
- Single-cell copy number calling and event history reconstruction.☆28Dec 21, 2024Updated last year
- scVI extension for unspliced RNA☆16May 18, 2025Updated 9 months ago
- This repository is for CellBin research group☆35Updated this week
- StereoMM is a graph fusion model that can integrate gene expression, histological images, and spatial location. And the information inter…☆38Dec 23, 2025Updated 2 months ago
- ☆52Oct 9, 2025Updated 4 months ago
- SPatial INtegration of spatially resolved transcriptomics datasets☆18Mar 14, 2025Updated 11 months ago