Alternatives and similar repositories for xCell

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

• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆197Updated 2 years ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆199Updated last month
• satijalab / azimuth
  A Shiny web app for mapping datasets using Seurat v4
  ☆144Updated last year
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆184Updated 3 weeks ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆140Updated 4 years ago
• zhangyuqing / ComBat-seq
  Batch effect adjustment based on negative binomial regression for RNA sequencing count data
  ☆201Updated 5 years ago
• huayc09 / SeuratExtend
  ☆202Updated 2 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆153Updated 3 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆185Updated 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
  ☆122Updated 2 years ago
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆133Updated last year
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆230Updated last year
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆237Updated 2 years ago
• 10XGenomics / loupeR
  Convert Seurat objects to 10x Genomics Loupe files.
  ☆148Updated this week
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆311Updated 3 years ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆215Updated last year
• kharchenkolab / pagoda2
  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
  ☆246Updated 5 months ago
• navinlabcode / copykat
  ☆269Updated 3 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆309Updated 3 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated 2 years ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆300Updated 2 years ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆183Updated last year
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆193Updated 2 months ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆99Updated 2 years ago
• tallulandrews / scRNASeqPipeline
  ☆118Updated 7 years ago
• SGDDNB / ShinyCell
  Shiny Interactive Web Apps for Single-Cell Data
  ☆203Updated 9 months ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆236Updated last month
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆260Updated 3 months ago
• neurorestore / Libra
  ☆181Updated 9 months ago
• mojaveazure / seurat-disk
  Interfaces for HDF5-based Single Cell File Formats
  ☆170Updated 2 years ago