Alternatives and similar repositories for pagoda2

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

• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆243Updated last year
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆201Updated 3 months ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆182Updated last week
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆213Updated last year
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆211Updated 11 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆229Updated 2 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆284Updated 2 years ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆281Updated last month
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆168Updated last year
• xuranw / MuSiC
  Multi-subject Single Cell Deconvolution
  ☆263Updated last year
• HelenaLC / muscat
  Multi-sample multi-group scRNA-seq analysis tools
  ☆194Updated 2 months ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆191Updated last month
• dviraran / xCell
  Cell types enrichment analysis
  ☆198Updated last year
• immunogenomics / presto
  Fast Wilcoxon and auROC
  ☆186Updated 8 months ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆192Updated 2 years ago
• enblacar / SCpubr
  Generate high quality, publication ready visualizations for single cell transcriptomics data.
  ☆199Updated last month
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆225Updated 2 months ago
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆202Updated 2 years ago
• navinlabcode / copykat
  ☆242Updated last year
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆186Updated 7 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆169Updated 2 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆178Updated last year
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆137Updated last year
• Oshlack / splatter
  Simple simulation of single-cell RNA sequencing data
  ☆228Updated this week
• neurorestore / Libra
  ☆172Updated 2 months ago
• satijalab / seurat-data
  Dataset distribution for Seurat
  ☆142Updated 4 months ago
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆298Updated last year
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆171Updated this week
• Dragonmasterx87 / Interactive-3D-Plotting-in-Seurat-3.0.0
  This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data
  ☆122Updated 2 years ago