R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
☆38Jan 13, 2026Updated 5 months ago
Alternatives and similar repositories for SpotClean
Users that are interested in SpotClean are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆30Jul 22, 2024Updated last year
- R package for distinguishing cells from background barcodes in droplet-based single-cell RNA-seq data☆12Apr 19, 2023Updated 3 years ago
- SpotGF: Denoising Spatially Resolved Transcriptomics Data Using an Optimal Transport-Based Gene Filtering Algorithm☆21Apr 8, 2025Updated last year
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics☆50Aug 18, 2025Updated 10 months ago
- 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
- 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.
- ☆135Feb 11, 2024Updated 2 years ago
- ☆31Mar 18, 2022Updated 4 years ago
- Code used to benchmark Xenium☆86Apr 10, 2026Updated 2 months ago
- BANKSY: spatial clustering☆156May 30, 2026Updated last month
- R package for Pathway RespOnsive GENe activity inference☆126Jan 30, 2023Updated 3 years ago
- ☆15Jun 27, 2025Updated last year
- Construct Tumor Transition Zone Microenvironment☆59Jun 25, 2025Updated last year
- Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning☆14Jun 28, 2026Updated last week
- ☆184May 4, 2026Updated 2 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆467Jan 22, 2026Updated 5 months ago
- Profile purification of single-cell spatial transcriptomics data☆51Jun 29, 2026Updated last week
- scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing and spatial dat…☆307Jul 1, 2026Updated last week
- STHD: probabilistic cell typing of Single spots in whole Transcriptome spatial data with High Definition☆38Apr 30, 2025Updated last year
- a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell …☆137Mar 22, 2023Updated 3 years ago
- Spatial omics analysis toolbox☆379Jun 2, 2026Updated last month
- Gene group activity utility functions for Scanpy☆108Dec 21, 2024Updated last year
- Spatial Cellular Estimator for Tumors☆65May 5, 2026Updated 2 months ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆99Dec 8, 2022Updated 3 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.
- mosaicMPI: mosaic multi-resolution program integration☆12May 13, 2026Updated last month
- Generate a spatial catalogue from multiplexed imaging data☆19Jun 12, 2025Updated last year
- DEPRECATED: Store and query public TCGA data☆11Sep 15, 2016Updated 9 years ago
- Axolotl Regenerative Telencehpalon Interpretation via Spatiotemporal Transcriptomic Atlas☆21Jul 3, 2022Updated 4 years ago
- ☆34Feb 25, 2025Updated last year
- Hotspot cluster distance analysis in spatial transcriptomic data☆37Feb 10, 2025Updated last year
- Use hodge decomposition for trajectory analysis☆26May 11, 2026Updated last month
- ☆132Mar 27, 2022Updated 4 years ago
- STRIDE (Spatial TRanscRIptomics DEconvolution by topic modelling) is a cell-type deconvolution tool for spatial transcriptomics by using …☆27Jan 23, 2024Updated 2 years 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.
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆23Jun 10, 2025Updated last year
- Methods for detecting doublets in single-cell sequencing data☆256Jun 23, 2026Updated 2 weeks ago
- Generate high quality, publication ready visualizations for single cell transcriptomics data.☆226Mar 2, 2026Updated 4 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆286Updated this week
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆82Feb 10, 2026Updated 4 months ago
- This repository contains code related to the publication "Comparative performance of the BGI and Illumina sequencing technology for singl…☆18Oct 12, 2021Updated 4 years ago
- ☆35Mar 16, 2026Updated 3 months ago