Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue"
☆32Nov 30, 2023Updated 2 years ago
Alternatives and similar repositories for janesick_nature_comms_2023_companion
Users that are interested in janesick_nature_comms_2023_companion 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 Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis☆19Apr 23, 2025Updated last year
- Suite of analysis tools for spatial total RNA-sequencing☆12Aug 10, 2023Updated 2 years ago
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆24Jun 10, 2025Updated 10 months ago
- CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data☆16Mar 13, 2026Updated last month
- ☆11Aug 10, 2023Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆37Oct 22, 2025Updated 6 months ago
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆18Sep 19, 2025Updated 7 months ago
- Repository for all R scripts used for the bioinformatic analyses of the mouse and human 10x Genomics Visium spatially resolved transcript…☆33Jul 13, 2024Updated last year
- R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients☆34Apr 9, 2026Updated 2 weeks ago
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆114Jun 9, 2025Updated 10 months ago
- Probabilistic Alignment of Spatial Transcriptomics Experiments v.2☆43Mar 2, 2025Updated last year
- Code used to benchmark Xenium☆80Apr 10, 2026Updated 2 weeks ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆167Updated this week
- ☆20May 1, 2023Updated 2 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- R functions underlying ExpressAnalyst☆14Apr 21, 2026Updated last week
- Interoperability between SpatialData and the Xenium Explorer☆25Jul 31, 2024Updated last year
- Code for the spatial transcriptomic paper on IPF lungs☆22Jul 18, 2024Updated last year
- GitKraken lesson (forked from HBS-RCS)☆10Mar 20, 2026Updated last month
- ☆12May 29, 2024Updated last year
- ☆45Feb 13, 2026Updated 2 months ago
- ☆43Apr 13, 2026Updated 2 weeks ago
- Test genes for Spatial Variation☆15Dec 20, 2024Updated last year
- R package for easy interop between Perseus and R☆17Sep 9, 2022Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Super-resolved spatial transcriptomics by deep data fusion☆74Mar 30, 2023Updated 3 years ago
- An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.☆16Aug 6, 2019Updated 6 years ago
- Import Trackmate XML files in Python as Pandas dataframe☆12Mar 1, 2025Updated last year
- Spatial Single-Cell Analysis Toolkit☆111Mar 11, 2026Updated last month
- Computer simulator of multiplex tissue images from a set of user-defined parameters☆10Dec 13, 2022Updated 3 years ago
- ☆13Sep 30, 2024Updated last year
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆15Feb 27, 2026Updated 2 months ago
- Bayesian Analytics for Spatial Segmentation☆31May 4, 2025Updated 11 months ago
- ☆13May 28, 2025Updated 11 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.
- ☆10Feb 12, 2019Updated 7 years ago
- Issues and pull requests for BiocStyle should go here.☆14Oct 30, 2025Updated 5 months ago
- The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains☆34Apr 11, 2025Updated last year
- A flexible parser generator producing output from object-oriented hierarchical context-free grammar specifications.☆12Nov 16, 2021Updated 4 years ago
- Codebase for the paper Zucha et al. titled "Spatiotemporal transcriptomic map of glial cell response in mouse model of acute brain ischem…☆15Oct 23, 2024Updated last year
- Spatial omics analysis and visualization library☆25Updated this week
- ☆21May 6, 2025Updated 11 months ago