☆29Mar 13, 2026Updated last week
Alternatives and similar repositories for spatialxe
Users that are interested in spatialxe are comparing it to the libraries listed below
Sorting:
- Python API and Jupyter widget for Vitessce☆62Feb 12, 2026Updated last month
- An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.☆14Nov 3, 2025Updated 4 months ago
- Extension of SpatialExperiment with sf☆57Mar 7, 2026Updated 2 weeks ago
- Compute the neighborhood consolidation matrix and identify SHRs☆13Jun 12, 2025Updated 9 months ago
- FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.☆13Dec 6, 2025Updated 3 months ago
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Feb 6, 2026Updated last month
- Integration of gut cell atlases☆34Oct 29, 2025Updated 4 months ago
- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…☆72Updated this week
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆88Mar 11, 2026Updated last week
- Accelerated genomics workflows in NextFlow☆42Sep 11, 2024Updated last year
- BANKSY: spatial clustering☆137Oct 15, 2025Updated 5 months ago
- ☆10May 31, 2022Updated 3 years ago
- GIve easy, high-level access to ome-zarr fileset☆22Sep 22, 2025Updated 5 months ago
- Single Cell Analysis Operations☆13Nov 25, 2025Updated 3 months ago
- Interactive and integrated analysis of multiplexed tissue microarrays☆14Mar 9, 2026Updated last week
- A framework for performing single-cell and bulk read full-length analysis of mutations and splicing.☆53Feb 19, 2026Updated last month
- Generation of disentangled microenvironment-induced and intrinsic gene expression vectors from spatial transcriptomics data☆26Updated this week
- Python package to interactively annotate histological images within a jupyter notebook☆18Oct 20, 2025Updated 5 months ago
- An R package for performing cell typing in SMI and other single cell data☆48May 19, 2025Updated 10 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆267Updated this week
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆55Nov 13, 2025Updated 4 months ago
- A single cell transcriptomics pipeline for QC, integration and making the data presentable☆91Updated this week
- Convert your single-cell/spatial analyses to parallel HPC/cloud workflows just using pipes in R☆17Dec 18, 2024Updated last year
- This is a repository of IAMSAM, an image-based ST analysis tool☆22Jun 24, 2025Updated 8 months ago
- Python project containing Ice remoting code for OMERO☆28Feb 17, 2026Updated last month
- An introduction to OME-Zarr for big bioimaging data☆24Mar 13, 2026Updated last week
- An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter☆14Jan 18, 2019Updated 7 years ago
- Weakly supervised learning uncovers phenotypic signatures in single-cell data☆38Dec 17, 2025Updated 3 months ago
- A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, i…☆28Mar 14, 2025Updated last year
- ☆91Updated this week
- Ngio is a Python library to streamline OME-Zarr image analysis workflows.☆47Updated this week
- Analysis of imbalanced data and its impacts in a scRNA-seq integration setting☆31Mar 7, 2025Updated last year
- Probabilistic pseudotime for single-cell RNA-seq data☆11Oct 6, 2017Updated 8 years ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆159Mar 13, 2026Updated last week
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆17Sep 19, 2025Updated 6 months ago
- R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients☆31May 1, 2025Updated 10 months ago
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆40Mar 10, 2026Updated last week
- A repository for benchmarking spatial deconvolution and mapping tools☆36May 13, 2025Updated 10 months ago
- Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms☆47Oct 22, 2025Updated 5 months ago