Alternatives and similar repositories for cellassign

Users that are interested in cellassign 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.
  ☆168Updated 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
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆139Updated 2 years ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆188Updated this week
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆181Updated last year
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆171Updated last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆177Updated 2 years ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆151Updated last year
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆148Updated 3 years ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆159Updated last month
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆189Updated 11 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆166Updated 2 months ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆215Updated last year
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆139Updated 3 years ago
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆119Updated last year
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆168Updated 2 years ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆221Updated last year
• kharchenkolab / numbat
  Haplotype-aware CNV analysis from single-cell RNA-seq
  ☆195Updated this week
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆193Updated 2 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆168Updated 7 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆233Updated 2 years ago
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆189Updated 3 years ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆196Updated last week
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆113Updated last year
• dviraran / xCell
  Cell types enrichment analysis
  ☆203Updated last year
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆133Updated last year
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆212Updated this week
• cole-trapnell-lab / garnett
  Automated cell type classification
  ☆112Updated 9 months ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆146Updated 2 months ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆97Updated 2 years ago