hubmapconsortium / spatial-transcriptomics-pipelineLinks
☆29Updated last year
Alternatives and similar repositories for spatial-transcriptomics-pipeline
Users that are interested in spatial-transcriptomics-pipeline are comparing it to the libraries listed below
Sorting:
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆86Updated last month
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆65Updated 6 months ago
- A probabilistic cell typing algorithm for spatial transcriptomics.☆25Updated 2 months ago
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Updated 7 months ago
- Single-cell spatial proteomics analysis that makes you happy!☆49Updated this week
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Updated 3 weeks ago
- Python package for Probe set selection for targeted spatial transcriptomics.☆48Updated 2 months ago
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆39Updated 3 weeks ago
- ☆64Updated last week
- Interactive visualization of spatial omics data☆73Updated last week
- An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.☆29Updated 3 weeks ago
- ☆86Updated this week
- Identification of spatial homogeneous regions☆21Updated 3 months ago
- Spatial Single-Cell Analysis Toolkit☆106Updated last week
- Image Mass Cytometry analysis pipeline☆26Updated 7 months ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆24Updated this week
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆35Updated last year
- ☆24Updated last month
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆104Updated this week
- ☆27Updated last year
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆65Updated last month
- Interoperability between SpatialData and the Xenium Explorer☆25Updated last year
- ☆40Updated this week
- Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.☆50Updated 4 years ago
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆56Updated 6 months ago
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆82Updated last month
- MERlin is an extensible analysis pipeline applied to decoding MERFISH data☆35Updated 4 years ago
- Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effe…☆42Updated last year
- Python API and Jupyter widget for Vitessce☆60Updated 2 months ago
- 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