Alternatives and similar repositories for PhenoGraph

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

• scverse / scanpy_usage
  Scanpy use cases.
  ☆86Updated 4 years ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆169Updated last year
• dpeerlab / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆70Updated 4 years ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆175Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆145Updated 8 months ago
• rajewsky-lab / novosparc
  ☆131Updated last year
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• KrishnaswamyLab / SingleCellWorkshop
  ☆93Updated 4 years ago
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆225Updated 5 years ago
• 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
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆213Updated last year
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆213Updated last year
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆111Updated 9 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆167Updated last year
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆138Updated this week
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆172Updated last year
• hemberg-lab / SC3
  A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
  ☆127Updated 4 years ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆202Updated 6 months ago
• bioFAM / MOFA
  Multi-Omics Factor Analysis
  ☆249Updated 4 years ago
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆172Updated 4 months ago
• AllonKleinLab / SPRING
  ☆69Updated 7 years ago
• calico / solo
  software to detect doublets
  ☆94Updated 7 months ago
• Novartis / cellxgene-gateway
  Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cel…
  ☆65Updated last year
• linnarsson-lab / loompy
  Python implementation of the Loom file format - http://loompy.org
  ☆146Updated 8 months ago
• campbio / celda
  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
  ☆149Updated 6 months ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆138Updated 2 years ago
• AllonKleinLab / SPRING_dev
  ☆70Updated last year
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆112Updated 10 months ago
• epierson9 / ZIFA
  Zero-inflated dimensionality reduction algorithm for single-cell data
  ☆110Updated 5 years ago