Alternatives and similar repositories for CellChat

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

• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆633Updated 6 months ago
• crazyhottommy / scRNAseq-analysis-notes
  scRNAseq analysis notes from Ming Tang
  ☆733Updated 8 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆448Updated last month
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆727Updated last week
• hbctraining / Intro-to-scRNAseq
  ☆618Updated 4 months ago
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆548Updated last year
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆559Updated last month
• cole-trapnell-lab / monocle3
  ☆401Updated last month
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆485Updated 5 months ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆596Updated 9 months ago
• hbctraining / scRNA-seq
  ☆575Updated 4 years ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆419Updated 2 months ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆533Updated 2 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆431Updated 6 months ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆464Updated last year
• Teichlab / cellphonedb
  ☆356Updated 3 years ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆499Updated 3 weeks ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆385Updated this week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆435Updated last year
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆342Updated 9 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆426Updated 2 weeks ago
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆675Updated 3 years ago
• junjunlab / scRNAtoolVis
  Useful functions to make your scRNA-seq plot more cool!
  ☆356Updated 3 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆419Updated this week
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆994Updated last month
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆391Updated last month
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆430Updated last month
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆435Updated 9 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆345Updated 2 weeks ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆461Updated 6 months ago