Spatial analysis toolkit for single cell multiplexed tissue data
β30Sep 2, 2024Updated last year
Alternatives and similar repositories for SpatialTis
Users that are interested in SpatialTis are comparing it to the libraries listed below
Sorting:
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics π₯π¬β¨β56Jun 25, 2025Updated 8 months ago
- R package: ConDecon is a clustering-independent deconvolution method for estimating cell abundances in bulk tissues using single-cell RNAβ¦β13Oct 17, 2024Updated last year
- Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)β309Feb 3, 2026Updated last month
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.β31May 27, 2025Updated 9 months ago
- β13Dec 15, 2021Updated 4 years ago
- A quantitative framework for evaluating data structure preservation by dimensionality reduction techniquesβ16Jun 1, 2021Updated 4 years ago
- ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methodsβ13Jan 10, 2024Updated 2 years ago
- Bayesian Segmentation of Spatial Transcriptomics Dataβ202Dec 10, 2024Updated last year
- An interface for Nested Stochastic Block Model for single cell analysisβ37Sep 30, 2025Updated 5 months ago
- Spatial Single-Cell Analysis Toolkitβ110Mar 11, 2026Updated last week
- Microscopy Image Cytometry Toolkitβ114Jul 15, 2022Updated 3 years ago
- Accessible and interoperable whole slide image analysisβ189Mar 9, 2026Updated last week
- RAnking Markers for CEll Segmentationβ12Feb 22, 2022Updated 4 years ago
- A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.β16Updated this week
- Publically accessible code for DIISCO methodβ12Oct 15, 2025Updated 5 months ago
- Automatically annotate cell types, consistently across samples.β19Updated this week
- Package for the analysis of Transcripts outside segmented cells in ST dataβ28Mar 9, 2026Updated last week
- β49Mar 12, 2026Updated last week
- A simple native R reader for Zarr Arraysβ48Updated this week
- Flow & mass cytometry analytics.β60Updated this week
- Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.β18Jun 9, 2025Updated 9 months ago
- Pydantic models for OME-NGFFβ24Sep 14, 2025Updated 6 months ago
- Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"β21Nov 27, 2025Updated 3 months ago
- Static plotting for spatialdataβ75Updated this week
- Imaris file format readerβ14Aug 20, 2025Updated 7 months ago
- ClusterMap for multi-scale clustering analysis of spatial gene expressionβ46Jun 13, 2025Updated 9 months ago
- ATAC-seq lab for BIOINF525β10Mar 31, 2016Updated 9 years ago
- β21Mar 22, 2023Updated 3 years ago
- Image registration (alignment) software for large microscopy imagesβ27Oct 15, 2023Updated 2 years ago
- Tools for generating single-cell gene expression dataβ34Jun 20, 2025Updated 9 months ago
- Single-Cell Spatial Explorerβ15Dec 14, 2023Updated 2 years ago
- SignalingProfiler is a pipeline that builds signaling networks to cellular phenotypes from multiomics data.β15Oct 17, 2025Updated 5 months ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)β422Updated this week
- Single-cell spatial omics analysis that makes you happy!β52Updated this week
- CAST packageβ43Oct 26, 2024Updated last year
- Conditional Autoencoders for Multiplexed Pixel Analysisβ18Nov 25, 2022Updated 3 years ago
- STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics dataβ13Apr 1, 2024Updated last year
- Lab for quantitative bioimage analysis experiments in Pythonβ19Feb 16, 2026Updated last month
- R package to use EaSIeR to predict anti-tumor immune response from bulk RNA-seqβ15Dec 1, 2025Updated 3 months ago