Alternatives and similar repositories for PhenoGraph:

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

• dpeerlab / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆68Updated 4 years ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆81Updated 4 years ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆157Updated 9 months ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆152Updated last year
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆211Updated 4 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆98Updated last year
• rajewsky-lab / novosparc
  ☆126Updated last year
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆204Updated 11 months ago
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆110Updated 2 months ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆196Updated last year
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆163Updated 8 months ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆141Updated 2 months ago
• KrishnaswamyLab / SingleCellWorkshop
  ☆91Updated 4 years ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆155Updated last year
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆105Updated last week
• kharchenkolab / pagoda2
  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
  ☆222Updated 11 months ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆139Updated 4 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆62Updated last year
• AllonKleinLab / SPRING_dev
  ☆67Updated 9 months ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆52Updated 8 months ago
• almaan / stereoscope
  Spatial mapping of cell types by integration of transcriptomics data
  ☆89Updated 2 years ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆193Updated 10 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆127Updated 2 years ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆121Updated 3 months ago
• campbio / celda
  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
  ☆147Updated this week
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆190Updated last year
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆164Updated last year
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆106Updated 3 months ago
• 10XGenomics / single-cell-3prime-paper
  ☆84Updated 4 years ago
• hemberg-lab / SC3
  A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
  ☆122Updated 3 years ago