Alternatives and similar repositories for CellChat:

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

• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆479Updated 10 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆457Updated 3 weeks ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆418Updated last year
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆329Updated 4 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆413Updated 2 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆532Updated last week
• Teichlab / cellphonedb
  ☆353Updated 3 years ago
• cole-trapnell-lab / monocle3
  ☆377Updated 3 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆292Updated 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.
  ☆380Updated 3 months ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆605Updated 2 months ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆355Updated 3 weeks ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆441Updated last year
• IanevskiAleksandr / sc-type
  ☆260Updated 5 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆317Updated last year
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆407Updated 3 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆482Updated last week
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆352Updated 10 months ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆396Updated 2 weeks ago
• cellgeni / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆134Updated 2 years ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆329Updated 3 weeks ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆320Updated 9 months ago
• quadbio / scRNAseq_analysis_vignette
  Tutorial for scRNA-seq data analysis beginners using R
  ☆190Updated last month
• navinlabcode / copykat
  ☆230Updated 9 months ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆363Updated 3 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆268Updated 2 years ago
• samuel-marsh / scCustomize
  R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆249Updated last week
• junjunlab / scRNAtoolVis
  Useful functions to make your scRNA-seq plot more cool!
  ☆331Updated 3 months ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆563Updated 5 months ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆208Updated last week