Alternatives and similar repositories for SoupX:

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

• 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.
  ☆247Updated last week
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆185Updated last month
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆138Updated 3 years ago
• navinlabcode / copykat
  ☆228Updated 9 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆226Updated last year
• neurorestore / Libra
  ☆163Updated 7 months ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆221Updated 3 months ago
• IanevskiAleksandr / sc-type
  ☆257Updated 4 months ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆196Updated 7 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆142Updated 2 months ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆196Updated 6 months ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆185Updated 2 weeks ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆194Updated 10 months ago
• sunduanchen / Scissor
  Scissor package
  ☆214Updated 10 months ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆268Updated last month
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆176Updated 4 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆318Updated 8 months ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆182Updated this week
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆140Updated 3 years ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆292Updated 4 years ago
• carmonalab / UCell
  Gene set scoring for single-cell data
  ☆147Updated 5 months ago
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆122Updated 11 months ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆152Updated 2 years ago
• HelenaLC / muscat
  Multi-sample multi-group scRNA-seq analysis tools
  ☆184Updated last week
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆161Updated 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
  ☆121Updated 2 years ago
• enblacar / SCpubr
  Generate high quality, publication ready visualizations for single cell transcriptomics data.
  ☆179Updated last month
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆362Updated 4 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆272Updated 6 months ago
• velocyto-team / velocyto.R
  RNA velocity estimation in R
  ☆186Updated last year