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
  ☆454Updated last year
• 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
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆445Updated 11 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆322Updated 2 years ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆425Updated last week
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆614Updated 2 months ago
• cole-trapnell-lab / monocle3
  ☆437Updated last month
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆464Updated 8 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆321Updated 5 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆311Updated 3 years ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆355Updated last week
• IanevskiAleksandr / sc-type
  ☆285Updated last year
• navinlabcode / copykat
  ☆269Updated 3 months ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆478Updated last year
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆523Updated 10 months ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆300Updated 2 years ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆362Updated 2 weeks ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆403Updated 3 weeks ago
• quadbio / scRNAseq_analysis_vignette
  Tutorial for scRNA-seq data analysis beginners using R
  ☆241Updated 11 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆436Updated 2 weeks ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆465Updated last month
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆486Updated last month
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆324Updated last year
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆535Updated 4 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆309Updated 3 months ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆407Updated 5 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆237Updated 2 years ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆338Updated this week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆451Updated last week
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆414Updated 5 months ago