saeyslab / napari-sparrow
https://sparrow-pipeline.readthedocs.io/en/latest/
☆22Updated 3 weeks ago
Related projects ⓘ
Alternatives and complementary repositories for napari-sparrow
- Analyzing cellular niches in spatial transcriptomics data☆27Updated 5 months ago
- VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps☆41Updated 8 months ago
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆44Updated last month
- Probabilistic cell segmentation for in situ spatial transcriptomics☆45Updated last week
- ☆37Updated 3 weeks ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆87Updated this week
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆36Updated 2 months ago
- ☆23Updated last month
- CAST package☆23Updated 2 weeks ago
- Gene group activity utility functions for Scanpy☆56Updated 3 months ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆24Updated last month
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆56Updated 4 months ago
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆19Updated 3 months ago
- An R package for performing cell typing in SMI and other single cell data☆29Updated 2 months ago
- Interoperability between SpatialData and the Xenium Explorer☆15Updated 3 months ago
- Code used to benchmark Xenium☆40Updated 4 months ago
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆49Updated last week
- An R package for handling and analysing imaging mass cytometry data☆21Updated 2 weeks ago
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆39Updated last week
- ☆47Updated last year
- Identification of spatial homogeneous regions☆18Updated last month
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆68Updated 11 months ago
- CeLEry: cell location recovery in single-cell RNA sequencing☆31Updated 6 months ago
- RNA-velocity informed embeddings for visualizing cellular trajectories☆43Updated 2 years ago
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆58Updated 2 years ago
- R package for pathway analysis in scRNA-seq data☆62Updated 2 months ago
- Spatial direct messaging detected by bivariate Moran☆24Updated this week
- Join subcellular Visium HD bins into cells☆52Updated last week
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆50Updated last month
- Multi-resolution Variational Inference☆22Updated last month