Alternatives and similar repositories for souporcell:

Users that are interested in souporcell 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
  ☆266Updated 2 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆169Updated 8 months ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆137Updated 3 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆161Updated last year
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆193Updated 6 months ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆197Updated 11 months ago
• navinlabcode / copykat
  ☆228Updated 8 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆140Updated 3 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
  ☆121Updated 2 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆226Updated last year
• kharchenkolab / numbat
  Haplotype-aware CNV analysis from single-cell RNA-seq
  ☆180Updated this week
• timoast / sinto
  Tools for single-cell data processing
  ☆122Updated 9 months ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆91Updated 2 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆156Updated 8 months ago
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆143Updated 9 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆314Updated 8 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆140Updated 2 months ago
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆209Updated 2 months ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆143Updated 4 years ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆209Updated 2 months ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆164Updated this week
• JiekaiLab / scTE
  ☆105Updated 11 months ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆184Updated this week
• neurorestore / Libra
  ☆162Updated 6 months ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆185Updated last month
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆196Updated 7 months ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆117Updated 2 years ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆151Updated 2 years ago
• broadinstitute / Drop-seq
  Java tools for analyzing Drop-seq data
  ☆125Updated last month
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆113Updated 6 months ago