Alternatives and similar repositories for CellphoneDB

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

• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆452Updated last year
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆535Updated 3 months ago
• Teichlab / cellphonedb
  ☆358Updated 4 years ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆450Updated 3 weeks ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆572Updated 7 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆611Updated 2 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆413Updated this week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆405Updated 5 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆485Updated last month
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆415Updated 2 weeks ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆375Updated 6 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆433Updated last week
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆234Updated last week
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆478Updated last year
• cole-trapnell-lab / monocle3
  ☆437Updated 3 weeks ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆263Updated last week
• IanevskiAleksandr / sc-type
  ☆285Updated last year
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆404Updated 4 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆463Updated last year
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆521Updated 10 months ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆465Updated 3 weeks ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆308Updated this week
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆444Updated 11 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆397Updated 2 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆425Updated last month
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆272Updated 2 months ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆245Updated 2 weeks ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆362Updated last week
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆342Updated 11 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆320Updated 5 years ago