Alternatives and similar repositories for PhenoGraph

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

• Teichlab / bbknn
  Batch balanced KNN
  ☆176Updated 2 years ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆86Updated 5 years ago
• dpeerlab / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆73Updated 5 years ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆136Updated 2 years ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆149Updated last year
• KrishnaswamyLab / SingleCellWorkshop
  ☆96Updated 4 years ago
• rajewsky-lab / novosparc
  ☆131Updated 2 years ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆178Updated last year
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆231Updated 5 years ago
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆174Updated 2 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆217Updated last year
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆218Updated 2 years ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆205Updated 2 months ago
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆112Updated 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…
  ☆109Updated last month
• klarman-cell-observatory / scPhere
  ☆101Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated last year
• hemberg-lab / SC3
  A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
  ☆128Updated 4 years ago
• campbio / celda
  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
  ☆151Updated 10 months ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆97Updated 6 years ago
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆143Updated last year
• Novartis / cellxgene-gateway
  Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cel…
  ☆66Updated 3 weeks ago
• AllonKleinLab / SPRING
  ☆69Updated 7 years ago
• epierson9 / ZIFA
  Zero-inflated dimensionality reduction algorithm for single-cell data
  ☆110Updated 5 years ago
• bioFAM / MOFA
  Multi-Omics Factor Analysis
  ☆253Updated 5 years ago
• KrishnaswamyLab / scprep
  A collection of scripts and tools for loading, processing, and handling single cell data.
  ☆76Updated 3 months ago
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆209Updated 2 years ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆160Updated 4 years ago
• dynverse / dynmethods
  A collection of 50+ trajectory inference methods within a common interface 📥📤
  ☆131Updated 2 years ago