Alternatives and similar repositories for spatialproteomics

Users that are interested in spatialproteomics are comparing it to the libraries listed below

• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆47Updated 2 weeks ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆80Updated last week
• scverse / spatialdata-io
  ☆65Updated last week
• scverse / spatialdata-notebooks
  ☆54Updated last week
• scverse / conference-2024
  Slides and Notebooks for scverse 2024
  ☆17Updated 10 months ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆34Updated last week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆29Updated this week
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆39Updated 3 weeks ago
• quadbio / cell-annotator
  Automatically annotate cell types, consistently across samples.
  ☆14Updated last week
• laminlabs / bionty
  Registries for basic biological entities, coupled to public ontologies.
  ☆16Updated this week
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• scverse / ecosystem-packages
  Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
  ☆25Updated last week
• scverse / spatialdata-plot
  Static plotting for spatialdata
  ☆62Updated last week
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆64Updated last month
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆18Updated 6 months ago
• Feanor007 / MESA
  A python package for Multiomics and Ecological Spatial Analysis (MESA)
  ☆20Updated 3 months ago
• scverse / pytometry
  Flow & mass cytometry analytics.
  ☆53Updated last week
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆53Updated last month
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆33Updated 3 weeks ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆24Updated last year
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆99Updated 2 months ago
• jkobject / scDataLoader
  a dataloader to work with large single cell datasets from lamindb
  ☆29Updated last month
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 6 months ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆27Updated 10 months ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆94Updated last month
• HiDiHlabs / ssam
  ☆27Updated 9 months ago
• MICS-Lab / scyan
  Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effe…
  ☆36Updated 8 months ago
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆74Updated last week
• vitessce / vitessce-python
  Python API and Jupyter widget for Vitessce
  ☆50Updated this week
• metaspace2020 / metaspace-converter
  Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
  ☆11Updated last year