TheJacksonLaboratory / STQLinks
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
☆22Updated 3 weeks ago
Alternatives and similar repositories for STQ
Users that are interested in STQ are comparing it to the libraries listed below
Sorting:
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆66Updated 3 weeks ago
- Spatial Single-Cell Analysis Toolkit☆105Updated 2 weeks ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆93Updated 2 years ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆46Updated last year
- Histology Topography Cytometry Analysis Toolbox☆69Updated 2 months ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆38Updated last year
- Integrated pipeline for multiplexed image analysis☆100Updated last week
- A pixel classification based multiplexed image segmentation pipeline☆103Updated 2 years ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆35Updated last year
- Sub-cellular spatial transcriptomics Cell Segmentation☆68Updated 2 years ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆39Updated 3 months ago
- Interactive visualization of spatial omics data☆73Updated last week
- A toolkit for processing multiplexed tissue images☆67Updated 2 weeks ago
- ☆15Updated 3 years ago
- ☆85Updated last week
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆11Updated 2 years ago
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆70Updated last year
- Multiple-choice microscopy pipeline☆144Updated last month
- ☆35Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆84Updated last month
- Python package for reading imaging mass cytometry (IMC) files☆18Updated last week
- ☆24Updated 8 months ago
- comseg☆24Updated 10 months ago
- Single-cell spatial proteomics analysis that makes you happy!☆48Updated this week
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆16Updated 4 years ago
- QuPath extension to interactively align images☆26Updated 4 months ago
- ☆34Updated last year
- A pipeline to transform images into valuable analysis items☆17Updated 6 months ago
- ☆42Updated 2 months ago
- ☆53Updated 4 years ago