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.
  ☆44Updated 4 years ago
• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆44Updated 6 months ago
• randel / MIND
  Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution
  ☆45Updated 2 years ago
• oganm / homologene
  An r package that works as a wrapper to homologene
  ☆45Updated last year
• Teichlab / cellity
  ☆37Updated 8 years ago
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆20Updated 2 years ago
• stemangiola / tidySingleCellExperiment
  Brings SingleCellExperiment objects to the tidyverse
  ☆36Updated 4 months ago
• kevinrue / velociraptor
  Toolkit for Single-Cell Velocity
  ☆55Updated 4 months ago
• Shians / CellBench
  R package for benchmarking single cell analysis methods
  ☆31Updated last year
• jgamache014 / snRNA-seq-workflow
  Human brain, >200,000 nuclei
  ☆24Updated 3 years ago
• shenorrLabTRDF / cellAlign
  ☆41Updated 4 years ago
• igrabski / scRNAseq-cell-type
  Probabilistic gene expression barcodes for cell type annotation
  ☆25Updated 3 years ago
• BaderLab / AgingMouseBrainCCInx
  Predicted cell-cell interactions of the aging mouse brain
  ☆20Updated 5 years ago
• rikenbit / scTensor
  R package for detection of cell-cell interaction using Non-negative Tensor Decomposition
  ☆34Updated 2 years ago
• SydneyBioX / scClassify
  Hierarchical classification of cells
  ☆23Updated 9 months ago
• stephaniehicks / scBatchPaper
  Code used for the single-cell RNA-Seq batch effects paper
  ☆10Updated 7 years ago
• korsunskylab / rcna
  R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)
  ☆15Updated last year
• immunogenomics / singlecellmethods
  Collection of useful methods for single cell analysis
  ☆14Updated 8 months ago
• pachterlab / BHGP_2022
  ☆21Updated 3 years ago
• bioturing / signac
  An analytics package for single cell data
  ☆22Updated 2 years ago
• stephaniehicks / spatialexperiment-analysis
  repo to explore spatial data in R/Bioconductor and Python
  ☆12Updated 5 years ago
• montilab / hypeR
  An R Package for Geneset Enrichment Workflows
  ☆76Updated last week
• anna-neufeld / countsplit
  ☆21Updated last year
• Oshlack / speckle
  R package for specialised analysis of single cell data
  ☆38Updated 2 years ago
• neurogenomics / reanalysis_Mathys_2019
  A re-analysis of the [Single-cell transcriptomic analysis of Alzheimer’s disease](https://www.nature.com/articles/s41586-019-1195-2) usin…
  ☆14Updated last year
• ati-lz / HCA_Benchmarking
  This repository contains HCA Benchmarking codes
  ☆26Updated 5 years ago
• powellgenomicslab / DropletQC
  Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
  ☆37Updated 3 years ago
• myles-lewis / glmmSeq
  Gene-level general linear mixed model
  ☆21Updated 3 months ago
• LTLA / basilisk
  Clone of the Bioconductor repository for the basilisk package.
  ☆27Updated this week
• NBISweden / single-cell_sib_scilifelab
  SIB/Scilifelab autumn school in single cell omics 2019.
  ☆22Updated 5 years ago