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 🖥🔬✨
  ☆55Updated 3 months ago
• jacoblevine / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆137Updated 4 years ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆171Updated last year
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆99Updated 3 months ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• BodenmillerGroup / ImcSegmentationPipeline
  A pixel classification based multiplexed image segmentation pipeline
  ☆101Updated last year
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆88Updated last year
• ElementoLab / utag
  ☆39Updated last year
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆49Updated 3 years ago
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆67Updated 11 months ago
• bioFAM / mofax
  Work with trained factor models in Python
  ☆35Updated 11 months ago
• shuxiaoc / maxfuse
  ☆55Updated last year
• LieberInstitute / spatialLIBD
  Code for the spatialLIBD R/Bioconductor package and shiny app
  ☆96Updated last week
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆67Updated 2 years ago
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆97Updated 4 months ago
• klarman-cell-observatory / scPhere
  ☆102Updated 2 years ago
• TaylorResearchLab / scedar
  Single-cell exploratory data analysis for RNA-Seq
  ☆40Updated 4 years ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆83Updated 2 months ago
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆46Updated 3 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆137Updated 2 weeks ago
• ludvb / xfuse
  Super-resolved spatial transcriptomics by deep data fusion
  ☆74Updated 2 years ago
• lilab-bcb / harmony-pytorch
  ☆56Updated 4 months ago
• KrishnaswamyLab / SAUCIE
  ☆100Updated last year
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• raphael-group / paste
  Probabilistic Alignment of Spatial Transcriptomics Experiments
  ☆94Updated 7 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 7 months ago
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆70Updated 2 years ago
• willtownes / nsf-paper
  Nonnegative spatial factorization for multivariate count data
  ☆59Updated 2 years ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆64Updated 2 weeks ago
• BodenmillerGroup / cytomapper
  R package for visualization of highly multiplexed imaging data
  ☆33Updated 4 months ago