Alternatives and similar repositories for pagoda2:

Users that are interested in pagoda2 are comparing it to the libraries listed below

• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆157Updated 11 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆263Updated 2 years ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆181Updated this week
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆175Updated last week
• enblacar / SCpubr
  Generate high quality, publication ready visualizations for single cell transcriptomics data.
  ☆171Updated this week
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆187Updated 5 months ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆182Updated last week
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆216Updated 3 weeks ago
• HelenaLC / muscat
  Multi-sample multi-group scRNA-seq analysis tools
  ☆176Updated 3 months ago
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆229Updated last year
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆133Updated this week
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆155Updated last year
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆174Updated 2 months ago
• navinlabcode / copykat
  ☆219Updated 6 months ago
• neurorestore / Libra
  ☆159Updated 4 months ago
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆203Updated 10 months ago
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆163Updated 7 months ago
• ncborcherding / escape
  Easy single cell analysis platform for enrichment
  ☆157Updated last month
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆221Updated last year
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆136Updated 3 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.
  ☆236Updated 2 weeks ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆261Updated last month
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆192Updated 9 months ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆182Updated 4 months ago
• quadbio / Pando
  Multiome GRN inference.
  ☆115Updated 8 months ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆157Updated last month
• ncborcherding / scRepertoire
  A toolkit for single-cell immune profiling
  ☆320Updated last week
• dviraran / xCell
  Cell types enrichment analysis
  ☆191Updated 7 months ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆162Updated 6 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆139Updated 2 years ago