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
  ☆279Updated 2 years ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆139Updated 3 years ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆205Updated 8 months ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆93Updated 2 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆174Updated 10 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆163Updated last year
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆154Updated 5 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆140Updated 3 years ago
• neurorestore / Libra
  ☆169Updated 3 weeks ago
• navinlabcode / copykat
  ☆235Updated 11 months ago
• hbctraining / Investigating-chromatin-biology-ChIPseq
  ☆92Updated 3 weeks ago
• timoast / sinto
  Tools for single-cell data processing
  ☆124Updated last year
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆201Updated 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
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆215Updated 4 months ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆195Updated 2 months ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆197Updated last year
• JiekaiLab / scTE
  ☆107Updated last year
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆191Updated last week
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆147Updated 4 months ago
• kharchenkolab / numbat
  Haplotype-aware CNV analysis from single-cell RNA-seq
  ☆181Updated 2 weeks ago
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆126Updated last year
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆116Updated 8 months ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆204Updated 9 months ago
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆143Updated 11 months ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆151Updated 4 years ago
• bnprks / BPCells
  Scaling Single Cell Analysis to Millions of Cells
  ☆210Updated 2 weeks ago
• fl-yu / CUT-RUNTools-2.0
  CUT&RUN and CUT&Tag data processing and analysis
  ☆109Updated 2 months ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆224Updated last month
• AntonioDeFalco / SCEVAN
  R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the …
  ☆105Updated 2 months ago