Alternatives and similar repositories for scCODA

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

• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆116Updated 8 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆147Updated 4 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆160Updated 2 months ago
• quadbio / Pando
  Multiome GRN inference.
  ☆123Updated last year
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆94Updated 3 years ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆111Updated last month
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆174Updated last month
• neurorestore / Augur
  Cell type prioritization in single-cell data
  ☆119Updated 7 months ago
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆106Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆163Updated last year
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆204Updated 9 months ago
• carmonalab / GeneNMF
  Methods to discover gene programs on single-cell data
  ☆118Updated last month
• carmonalab / UCell
  Gene set scoring for single-cell data
  ☆150Updated 3 weeks ago
• timoast / sinto
  Tools for single-cell data processing
  ☆124Updated last year
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆129Updated 3 months ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆86Updated 11 months ago
• AntonioDeFalco / SCEVAN
  R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the …
  ☆105Updated 2 months ago
• martinjzhang / scDRS
  Single-cell disease relevance score (scDRS)
  ☆132Updated 7 months ago
• satijalab / azimuth
  A Shiny web app for mapping datasets using Seurat v4
  ☆127Updated 6 months ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆109Updated 3 weeks ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆95Updated last year
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆131Updated 6 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆73Updated 4 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆82Updated 2 weeks ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆140Updated 3 years ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆137Updated last year
• tanaylab / metacell
  Metacell - Single-cell mRNA Analysis
  ☆115Updated 4 months ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆152Updated last year
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆101Updated 8 months ago
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆68Updated 10 months ago