Alternatives and similar repositories for SC3

Users that are interested in SC3 are comparing it to the libraries listed below

• cole-trapnell-lab / garnett
  Automated cell type classification
  ☆112Updated 9 months ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆193Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆168Updated last year
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆181Updated last year
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆139Updated 2 years ago
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆86Updated 6 years ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆183Updated last month
• kharchenkolab / pagoda2
  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
  ☆238Updated 2 months ago
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆143Updated last year
• scverse / scanpy_usage
  Scanpy use cases.
  ☆87Updated 5 years ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆97Updated 2 years ago
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆207Updated 2 years ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆95Updated 6 years ago
• satijalab / azimuth
  A Shiny web app for mapping datasets using Seurat v4
  ☆134Updated 11 months ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆113Updated last year
• 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
• Oshlack / splatter
  Simple simulation of single-cell RNA sequencing data
  ☆231Updated 2 months ago
• tallulandrews / scRNASeqPipeline
  ☆118Updated 7 years ago
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆215Updated last year
• campbio / celda
  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
  ☆151Updated 8 months ago
• broadinstitute / Drop-seq
  Java tools for analyzing Drop-seq data
  ☆130Updated 2 weeks ago
• kharchenkolab / dropEst
  Pipeline for initial analysis of droplet-based single-cell RNA-seq data
  ☆93Updated 3 years ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆203Updated last year
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆95Updated 4 years ago
• YeoLab / single-cell-bioinformatics
  Course material in notebook format for learning about single cell bioinformatics methods
  ☆99Updated 9 years ago
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆189Updated 3 years ago
• hms-dbmi / scde
  R package for analyzing single-cell RNA-seq data
  ☆176Updated last year
• AllonKleinLab / SPRING
  ☆69Updated 7 years ago
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆97Updated 4 years ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆152Updated last year