zijianni / SpotCleanView external linksLinks
R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
☆35Jan 13, 2026Updated last month
Alternatives and similar repositories for SpotClean
Users that are interested in SpotClean are comparing it to the libraries listed below
Sorting:
- general repo that holds all analysis and figures for the thymus spatial atlas by Yayon, Kedlian, Boehme, Radtke and many more!☆12Nov 20, 2024Updated last year
- R package for distinguishing cells from background barcodes in droplet-based single-cell RNA-seq data☆11Apr 19, 2023Updated 2 years ago
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆30Jul 22, 2024Updated last year
- SpotGF: Denoising Spatially Resolved Transcriptomics Data Using an Optimal Transport-Based Gene Filtering Algorithm☆21Apr 8, 2025Updated 10 months ago
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics☆46Aug 18, 2025Updated 5 months ago
- ☆129Feb 11, 2024Updated 2 years ago
- ☆27Mar 18, 2022Updated 3 years ago
- Code used to benchmark Xenium☆75Jun 30, 2024Updated last year
- R package for Pathway RespOnsive GENe activity inference☆114Jan 30, 2023Updated 3 years ago
- BANKSY: spatial clustering☆136Oct 15, 2025Updated 3 months ago
- Profile purification of single-cell spatial transcriptomics data☆28Nov 13, 2025Updated 3 months ago
- Axolotl Regenerative Telencehpalon Interpretation via Spatiotemporal Transcriptomic Atlas☆21Jul 3, 2022Updated 3 years ago
- Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning☆12Feb 6, 2026Updated last week
- Gene group activity utility functions for Scanpy☆100Dec 21, 2024Updated last year
- This repo is archived, the these workflows are still available in the GATK repository under the scripts directory. The workflows are also…☆11Mar 9, 2020Updated 5 years ago
- scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy…☆292Updated this week
- a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell …☆130Mar 22, 2023Updated 2 years ago
- Use hodge decomposition for trajectory analysis☆23Nov 12, 2025Updated 3 months ago
- Porting of Protein Activity and Pathway Inference to single cell and Python.☆12Feb 1, 2026Updated last week
- ☆181May 6, 2025Updated 9 months ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆438Jan 22, 2026Updated 3 weeks ago
- Construct Tumor Transition Zone Microenvironment☆53Jun 25, 2025Updated 7 months ago
- mosaicMPI: mosaic multi-resolution program integration☆12Dec 9, 2025Updated 2 months ago
- We describe a transcriptional reference map of human natural killer (NK) cells based on analysis of scRNA-seq data from both blood and ti…☆14Oct 7, 2024Updated last year
- STHD: probabilistic cell typing of Single spots in whole Transcriptome spatial data with High Definition☆36Apr 30, 2025Updated 9 months ago
- STRIDE (Spatial TRanscRIptomics DEconvolution by topic modelling) is a cell-type deconvolution tool for spatial transcriptomics by using …☆26Jan 23, 2024Updated 2 years ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆88Dec 8, 2022Updated 3 years ago
- Metacell - Single-cell mRNA Analysis☆120Jan 26, 2025Updated last year
- DEPRECATED: Store and query public TCGA data☆11Sep 15, 2016Updated 9 years ago
- Hotspot cluster distance analysis in spatial transcriptomic data☆35Feb 10, 2025Updated last year
- Spatial omics analysis toolbox☆360Updated this week
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆263Updated this week
- Methods for detecting doublets in single-cell sequencing data☆230Dec 15, 2025Updated last month
- ☆129Mar 27, 2022Updated 3 years ago
- Spatial Cellular Estimator for Tumors☆61Updated this week
- Framework for analysis of cell-types and Ligand-Receptor cooccurrences☆18Feb 13, 2023Updated 3 years ago
- ☆13Jul 16, 2024Updated last year
- ☆15Jun 27, 2025Updated 7 months ago
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆74Jun 13, 2025Updated 8 months ago