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
  ☆264Updated 2 years ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆189Updated 5 months ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆136Updated 3 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆158Updated last year
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆139Updated 3 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆165Updated 7 months ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆89Updated 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 last year
• neurorestore / Libra
  ☆162Updated 5 months ago
• JiekaiLab / scTE
  ☆104Updated 9 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆138Updated last month
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆183Updated this week
• dviraran / xCell
  Cell types enrichment analysis
  ☆191Updated 8 months ago
• kharchenkolab / numbat
  Haplotype-aware CNV analysis from single-cell RNA-seq
  ☆178Updated 2 months ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆193Updated 10 months ago
• broadinstitute / Drop-seq
  Java tools for analyzing Drop-seq data
  ☆124Updated last week
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆223Updated last year
• navinlabcode / copykat
  ☆225Updated 7 months ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆149Updated 2 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆154Updated 7 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆156Updated last year
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆204Updated 3 weeks ago
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆140Updated 8 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.
  ☆242Updated 2 weeks ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆140Updated 4 years ago
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆208Updated 3 weeks ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆124Updated 2 months ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆279Updated last year
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆181Updated this week
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆112Updated 5 months ago