Alternatives and similar repositories for scRNAseq

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

• LTLA / SingleCellThoughts
  Assorted thoughts, explanations and justifications for code in the scran package and the simpleSingleCell workflow.
  ☆47Updated 4 months ago
• randel / MIND
  Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution
  ☆47Updated 2 years ago
• epurdom / clusterExperiment
  R package of techniques for comparing clusterings of single-cell sequencing data
  ☆41Updated last year
• tidyomics / tidySingleCellExperiment
  Brings SingleCellExperiment objects to the tidyverse
  ☆37Updated 2 months ago
• milescsmith / ReductionWrappers
  R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)
  ☆36Updated last year
• SydneyBioX / scMerge
  Statistical approach for removing unwanted variation from multiple single-cell datasets
  ☆70Updated last year
• oganm / homologene
  An r package that works as a wrapper to homologene
  ☆49Updated 2 years ago
• plger / pipeComp
  A R framework for pipeline benchmarking, with application to single-cell RNAseq
  ☆42Updated 4 years ago
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆21Updated 3 years ago
• DavisLaboratory / singscore
  An R/Bioconductor package that implements a single-sample molecular phenotyping approach
  ☆46Updated 3 months ago
• kieranrcampbell / switchde
  Inference of switch-like differential expression along single-cell trajectories
  ☆22Updated 8 years ago
• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆47Updated 6 months ago
• shenorrLabTRDF / cellAlign
  ☆43Updated 5 years ago
• ctlab / LinSeed
  Linseed: LINear Subspace identification for gene Expresion Deconvolution
  ☆33Updated 5 months ago
• BaderLab / scClustViz
  Explore and share your scRNAseq clustering results
  ☆50Updated 2 years ago
• pachterlab / SpatialFeatureExperiment
  Extension of SpatialExperiment with sf
  ☆57Updated 3 weeks ago
• Oshlack / speckle
  R package for specialised analysis of single cell data
  ☆40Updated 3 years ago
• quon-titative-biology / scAlign
  A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batch…
  ☆38Updated 4 years ago
• bioturing / signac
  An analytics package for single cell data
  ☆22Updated 3 years ago
• powellgenomicslab / DropletQC
  Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
  ☆41Updated 4 years ago
• jgamache014 / snRNA-seq-workflow
  Human brain, >200,000 nuclei
  ☆23Updated 4 years ago
• Shians / CellBench
  R package for benchmarking single cell analysis methods
  ☆32Updated 2 years ago
• czbiohub-sf / tabula-muris-vignettes
  Examples analyses using the single-cell RNA-seq data from mouse cell atlases
  ☆22Updated 6 years ago
• mojaveazure / loomR
  An R-based interface for loom files
  ☆67Updated 5 years ago
• waldronlab / data-science-seminar
  Topics In Data Science and Bioinformatics
  ☆79Updated last year
• GregorySchwartz / tooManyCellsR
  An R wrapper for too-many-cells, for clustering single cells and analyzing cell clade relationships with colorful visualizations.
  ☆26Updated 5 years ago
• niaid / dsb
  Normalize CITEseq Data
  ☆67Updated 2 months ago
• SaskiaFreytag / cluster_benchmarking_code
  ☆16Updated 7 years ago
• markrobinsonuzh / scRNAseq_clustering_comparison
  A study to compare methods for clustering of scRNA-seq data
  ☆45Updated last year
• theislab / pseudodynamics
  Dynamic models for single-cell RNA-seq time series.
  ☆40Updated 7 years ago