Alternatives and similar repositories for PhenoGraph

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

• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆54Updated 2 months ago
• jacoblevine / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆137Updated 4 years ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆96Updated last month
• Teichlab / bbknn
  Batch balanced KNN
  ☆169Updated last year
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆86Updated last year
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆130Updated 2 weeks ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆67Updated 2 years ago
• shuxiaoc / maxfuse
  ☆55Updated last year
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆49Updated 3 years ago
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆46Updated 2 months ago
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆64Updated 9 months ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆62Updated 2 weeks ago
• BodenmillerGroup / ImcSegmentationPipeline
  A pixel classification based multiplexed image segmentation pipeline
  ☆100Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 6 months ago
• HiDiHlabs / ssam
  ☆27Updated 10 months ago
• bioFAM / mofax
  Work with trained factor models in Python
  ☆34Updated 10 months ago
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆99Updated 3 months ago
• ElementoLab / utag
  ☆38Updated last year
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆101Updated 4 months ago
• CaiGroup / seqFISH-PLUS
  ☆52Updated 4 years ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆82Updated last month
• scverse / spatialdata-notebooks
  ☆57Updated this week
• TaylorResearchLab / scedar
  Single-cell exploratory data analysis for RNA-Seq
  ☆40Updated 4 years ago
• BodenmillerGroup / cytomapper
  R package for visualization of highly multiplexed imaging data
  ☆33Updated 3 months ago
• ImmuneDynamics / Spectre
  A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
  ☆62Updated this week
• rajewsky-lab / novosparc
  ☆131Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆63Updated 3 weeks ago
• KrishnaswamyLab / scprep
  A collection of scripts and tools for loading, processing, and handling single cell data.
  ☆74Updated last month
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆69Updated 2 years ago