Alternatives and similar repositories for pagoda2

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

• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆185Updated this week
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated last year
• xuranw / MuSiC
  Multi-subject Single Cell Deconvolution
  ☆278Updated last year
• HelenaLC / muscat
  Multi-sample multi-group scRNA-seq analysis tools
  ☆215Updated 3 weeks ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆206Updated last year
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆257Updated 2 months ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆304Updated 3 weeks ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆227Updated last year
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆307Updated 3 years ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆180Updated last year
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆174Updated last year
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆199Updated last week
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆209Updated 3 years ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆245Updated 2 weeks ago
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆217Updated last year
• enblacar / SCpubr
  Generate high quality, publication ready visualizations for single cell transcriptomics data.
  ☆213Updated 2 weeks ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆236Updated 2 years ago
• 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
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆225Updated 3 weeks ago
• navinlabcode / copykat
  ☆259Updated 2 months ago
• carmonalab / UCell
  Gene set scoring for single-cell data
  ☆176Updated 2 months ago
• mojaveazure / seurat-disk
  Interfaces for HDF5-based Single Cell File Formats
  ☆170Updated 2 years ago
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆191Updated 2 months ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆140Updated 4 years ago
• immunogenomics / presto
  Fast Wilcoxon and auROC
  ☆203Updated last year
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆195Updated 2 years ago
• huayc09 / SeuratExtend
  ☆197Updated last month
• Oshlack / splatter
  Simple simulation of single-cell RNA sequencing data
  ☆232Updated 3 weeks ago
• satijalab / seurat-data
  Dataset distribution for Seurat
  ☆151Updated 10 months ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆185Updated last year