Alternatives and similar repositories for metacells

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

• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆158Updated last month
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆68Updated 2 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆73Updated last month
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆101Updated 8 months ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆104Updated last month
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆68Updated last month
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆127Updated 2 months ago
• tanaylab / metacell
  Metacell - Single-cell mRNA Analysis
  ☆114Updated 3 months ago
• saezlab / visium_heart
  Spatial transcriptomics of heart tissue
  ☆84Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated 11 months ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆73Updated 8 months ago
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆105Updated 2 years ago
• carmonalab / GeneNMF
  Methods to discover gene programs on single-cell data
  ☆115Updated 2 weeks ago
• YosefLab / popV
  ☆75Updated this week
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆77Updated 8 months ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆94Updated last year
• navinlabcode / CellTrek
  ☆118Updated 3 years ago
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆58Updated last year
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated last year
• quadbio / Pando
  Multiome GRN inference.
  ☆121Updated last year
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆71Updated 3 months ago
• ShobiStassen / VIA
  trajectory inference
  ☆98Updated 3 months ago
• ShellyCoder / cellcall
  inferring cell-cell communication from scRNA-seq of ligand-receptor
  ☆81Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆107Updated last week
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆174Updated 3 weeks ago
• timoast / sinto
  Tools for single-cell data processing
  ☆124Updated 11 months ago
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆61Updated 3 years ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆110Updated 2 weeks ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 6 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆81Updated last month