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
  ☆69Updated 4 years ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆161Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 6 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• scverse / scanpy_usage
  Scanpy use cases.
  ☆85Updated 4 years ago
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆167Updated 11 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆101Updated last year
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆170Updated last month
• rajewsky-lab / novosparc
  ☆130Updated last year
• KrishnaswamyLab / SingleCellWorkshop
  ☆90Updated 4 years ago
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆109Updated 6 months ago
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆211Updated last year
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆112Updated 7 months ago
• campbio / celda
  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
  ☆148Updated 3 months ago
• sandhya212 / BISCUIT_SingleCell_IMM_ICML_2016
  R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.
  ☆66Updated 7 years ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆163Updated 2 years ago
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆206Updated last year
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆170Updated last year
• dynverse / dynmethods
  A collection of 50+ trajectory inference methods within a common interface 📥📤
  ☆128Updated last year
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆140Updated last year
• AllonKleinLab / SPRING
  ☆68Updated 7 years ago
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆218Updated 5 years ago
• KrishnaswamyLab / scprep
  A collection of scripts and tools for loading, processing, and handling single cell data.
  ☆72Updated last year
• 10XGenomics / single-cell-3prime-paper
  ☆85Updated 4 years ago
• JCVenterInstitute / NSForest
  A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…
  ☆62Updated 2 weeks ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆68Updated 3 months ago
• AllonKleinLab / SPRING_dev
  ☆69Updated 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…
  ☆100Updated last month
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆134Updated this week
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆201Updated last year