Alternatives and similar repositories for harmony:

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

• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆535Updated last week
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆463Updated last month
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆416Updated 2 months ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆609Updated 3 months ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆330Updated 5 months ago
• cole-trapnell-lab / monocle3
  ☆380Updated 4 months ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆364Updated 3 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆484Updated last month
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆409Updated last week
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆487Updated 11 months ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆499Updated last year
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆404Updated last month
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆394Updated 3 weeks ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆419Updated last year
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆332Updated this week
• Teichlab / cellphonedb
  ☆353Updated 3 years ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆321Updated this week
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆294Updated 4 years ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆445Updated last year
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆283Updated 7 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆317Updated 2 years ago
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆371Updated 5 months ago
• cole-trapnell-lab / monocle-release
  ☆284Updated 2 years ago
• IanevskiAleksandr / sc-type
  ☆261Updated 5 months ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆697Updated 2 weeks ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆221Updated last week
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆288Updated 2 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆438Updated 2 months ago
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆291Updated last year
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆348Updated 4 months ago