Alternatives and similar repositories for SingleCellWorkshop:

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

• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆153Updated 6 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆109Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆141Updated last month
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆141Updated 10 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆124Updated last year
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆67Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆95Updated this week
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆83Updated 4 months ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆179Updated 4 years ago
• czbiohub-sf / tabula-muris-senis
  Tabula Muris Senis
  ☆100Updated last year
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆134Updated last year
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆149Updated 2 years ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆87Updated 5 years ago
• LocasaleLab / Single-Cell-Metabolic-Landscape
  Pipeline for exploring metebolic heterogeneity at single-cell resolution
  ☆73Updated 4 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆157Updated 11 months ago
• quadbio / scMultiome_analysis_vignette
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
  ☆50Updated 8 months ago
• saezlab / visium_heart
  Spatial transcriptomics of heart tissue
  ☆78Updated last year
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆83Updated 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.
  ☆192Updated 9 months 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 last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆155Updated last year
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆138Updated 4 years ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆139Updated 2 years ago
• martinjzhang / scDRS
  Single-cell disease relevance score (scDRS)
  ☆119Updated 3 months ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆113Updated this week
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆184Updated 2 years ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆89Updated last year
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆105Updated 2 months ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆119Updated 8 months ago
• rajewsky-lab / novosparc
  ☆126Updated last year