Alternatives and similar repositories for copykat

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

• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆279Updated 2 years ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆191Updated 2 weeks ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆206Updated 9 months ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆139Updated 3 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆227Updated 2 years ago
• czbiohub-sf / scell_lung_adenocarcinoma
  This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset
  ☆149Updated 4 years ago
• sunduanchen / Scissor
  Scissor package
  ☆222Updated last year
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆298Updated 4 years ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆158Updated 6 months 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.
  ☆261Updated last week
• IanevskiAleksandr / sc-type
  ☆268Updated 7 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆147Updated 5 months ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆225Updated last month
• neurorestore / Libra
  ☆172Updated last month
• enblacar / SCpubr
  Generate high quality, publication ready visualizations for single cell transcriptomics data.
  ☆198Updated 3 weeks ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆141Updated 3 years ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆208Updated 10 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆427Updated last year
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆128Updated last year
• velocyto-team / velocyto.R
  RNA velocity estimation in R
  ☆186Updated last year
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆203Updated last year
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆159Updated 2 years ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆285Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• junjunlab / GseaVis
  An implement R package to visualize GSEA results
  ☆172Updated 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
  ☆121Updated 2 years ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆278Updated last month
• dviraran / xCell
  Cell types enrichment analysis
  ☆198Updated last year
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆332Updated 11 months ago
• Danko-Lab / BayesPrism
  A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
  ☆192Updated 3 weeks ago