Alternatives and similar repositories for utility:

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

• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆67Updated 5 years ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆79Updated last year
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆103Updated 2 weeks ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆61Updated last year
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆64Updated 7 months ago
• rpolicastro / scProportionTest
  ☆60Updated last year
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆91Updated 3 years ago
• cellgeni / batchbench
  ☆46Updated 2 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆100Updated 5 months ago
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆62Updated 2 years ago
• Japrin / STARTRAC
  STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
  ☆94Updated last year
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆99Updated 2 years ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆96Updated 2 weeks ago
• BostonGene / MFP
  Mollecular Functional Portraits
  ☆36Updated 10 months ago
• cssmillie / ulcerative_colitis
  ☆60Updated 4 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆68Updated 3 weeks ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated last year
• cozygene / bisque
  An R toolkit for estimation of cell composition from bulk expression data
  ☆71Updated 3 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 8 months ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆89Updated last year
• timoast / sinto
  Tools for single-cell data processing
  ☆122Updated 8 months ago
• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆92Updated 4 years ago
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆102Updated 2 years ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆79Updated 6 months ago
• livnatje / ImmuneResistance
  This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources…
  ☆72Updated 6 years ago
• Coolgenome / iTALK
  ☆59Updated 5 years ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆72Updated 5 months ago
• cellgeni / STARsolo
  wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
  ☆50Updated this week
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆156Updated last year
• AntonioDeFalco / SCEVAN
  R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the …
  ☆98Updated this week