R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients
☆38Aug 10, 2026Updated 2 months ago
Alternatives and similar repositories for XeniumSpatialAnalysis
Users that are interested in XeniumSpatialAnalysis are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Interoperability between SpatialData and the Xenium Explorer☆27Jul 31, 2024Updated 2 years ago
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆19Sep 19, 2025Updated last year
- ☆13Jul 26, 2026Updated 3 months ago
- Neighborhood Non-Negative Matrix Factorization☆11Sep 24, 2026Updated last month
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆297Updated this week
- 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.
- ☆15Aug 17, 2023Updated 3 years ago
- Spatial neighbour-aware transcript cleanup for imaging-based spatial transcriptomics data (Xenium, MERSCOPE, CosMx). XeniumClean removes…☆21Jul 19, 2026Updated 3 months ago
- Code used to benchmark Xenium☆88Apr 10, 2026Updated 6 months ago
- Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration☆132Sep 24, 2026Updated last month
- Probabilistic cell segmentation for in situ spatial transcriptomics☆199Updated this week
- ImageJ / Fiji macro to automatically correct white balance in RGB images☆16Nov 13, 2017Updated 8 years ago
- H&E to Xenium SIFT-based Alignment (HEX-SIFT). Automatic alignment of H&E images to a dapi image. Used for H&E alignment to Xenium dapi i…☆13Oct 13, 2026Updated 2 weeks ago
- ☆19Oct 2, 2023Updated 3 years ago
- ☆11Jun 12, 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.
- Shell wrappers for bulk and 10X single cell NGS pipelines, RNAseq, ChIPseq, ATACseq, CUT&RUN/TAG, GWAS, etc.☆17Oct 12, 2026Updated 3 weeks ago
- ☆18Sep 16, 2023Updated 3 years ago
- Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spat…☆35Nov 30, 2023Updated 2 years ago
- ☆30Jan 31, 2026Updated 9 months ago
- NeoDisc - A computational pipeline for the identification and prioritization of immunogenic tumor-specific HLA-I and -II antigens from ge…☆13Oct 8, 2024Updated 2 years ago
- An R package to implement Differential Gene Set Enrichment Analysis (DGSEA): A statistical approach to quantify the relative enrichment o…☆15Apr 12, 2023Updated 3 years ago
- Run DeepCell Applications☆10Apr 19, 2023Updated 3 years ago
- Scripts and datasets to reproduce the experiment of the paper "Exploring non-coding RNA functions with deep learning tools"☆16Mar 24, 2021Updated 5 years ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆61Aug 13, 2026Updated 2 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆54Jun 8, 2022Updated 4 years ago
- scRNA analysis of public dataset on bladder cancer☆20Dec 12, 2025Updated 10 months ago
- ☆14Jan 2, 2024Updated 2 years ago
- Single Cell Pretrained Regulatory network INference from Transcripts☆11Sep 17, 2024Updated 2 years ago
- ☆15May 19, 2022Updated 4 years ago
- ☆24Mar 22, 2023Updated 3 years ago
- Extension of SpatialExperiment with sf☆58Oct 22, 2026Updated last week
- Pipeline to detect HLA disruption from WES and RNAseq data☆23Feb 17, 2025Updated last year
- ☆144Feb 13, 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 comprehensive tool to infer TF-centred, spatial gene regulatory networks for the spatially resolved transcriptomic data.☆23Apr 27, 2025Updated last year
- ☆14Nov 12, 2025Updated 11 months ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆104Jul 4, 2026Updated 3 months ago
- We provided a step-by-step guide for performing colocalization analysis using the coloc package in R.☆11Nov 17, 2023Updated 2 years ago
- Introduction to Python3☆11Oct 26, 2020Updated 6 years ago
- ☆26Jul 2, 2024Updated 2 years ago
- popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and de…☆25Dec 3, 2025Updated 10 months ago