Alternatives and similar repositories for scRNAseq

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

• randel / MIND
  Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution
  ☆45Updated 2 years ago
• LTLA / SingleCellThoughts
  Assorted thoughts, explanations and justifications for code in the scran package and the simpleSingleCell workflow.
  ☆44Updated 4 years ago
• oganm / homologene
  An r package that works as a wrapper to homologene
  ☆46Updated last year
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆20Updated 2 years ago
• stephaniehicks / spatialexperiment-analysis
  repo to explore spatial data in R/Bioconductor and Python
  ☆12Updated 5 years ago
• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆44Updated 8 months ago
• stemangiola / tidySingleCellExperiment
  Brings SingleCellExperiment objects to the tidyverse
  ☆36Updated 6 months ago
• immunogenomics / singlecellmethods
  Collection of useful methods for single cell analysis
  ☆14Updated 10 months ago
• ctlab / LinSeed
  Linseed: LINear Subspace identification for gene Expresion Deconvolution
  ☆30Updated last month
• shenorrLabTRDF / cellAlign
  ☆41Updated 4 years ago
• Teichlab / cellity
  ☆37Updated 8 years ago
• anna-neufeld / countsplit
  ☆21Updated last year
• Simon-Leonard / FlexDotPlot
  R package for Flexible dot plots
  ☆29Updated 3 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
• kevinrue / velociraptor
  Toolkit for Single-Cell Velocity
  ☆56Updated 5 months ago
• bioturing / signac
  An analytics package for single cell data
  ☆22Updated 3 years ago
• rikenbit / scTensor
  R package for detection of cell-cell interaction using Non-negative Tensor Decomposition
  ☆34Updated last week
• dynverse / dynguidelines
  Selecting the optimal trajectory inference based on a given dataset and user input 🔮
  ☆18Updated 4 years ago
• SydneyBioX / scClassify
  Hierarchical classification of cells
  ☆23Updated 10 months ago
• jgamache014 / snRNA-seq-workflow
  Human brain, >200,000 nuclei
  ☆24Updated 4 years ago
• LTLA / basilisk
  Clone of the Bioconductor repository for the basilisk package.
  ☆27Updated last month
• PoolLab / generecovery
  ☆29Updated 2 years ago
• waldronlab / HGNChelper
  Identify and correct invalid gene symbols
  ☆58Updated 7 months ago
• kdzimm / PseudoreplicationPaper
  Code used to carry out parameter estimation, correlation estimation, type 1 error analysis, and power analysis for our "Pseudoreplication…
  ☆20Updated 4 years ago
• korsunskylab / rcna
  R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)
  ☆15Updated last year
• powellgenomicslab / DropletQC
  Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
  ☆38Updated 3 years ago
• pachterlab / concordexR
  Compute the neighborhood consolidation matrix and identify SHRs
  ☆13Updated 2 weeks ago
• markrobinsonuzh / cytofWorkflow
  ☆16Updated last year
• Drinchai / BloodGen3Module
  This R package for performing module repertoire analyses and generating fingerprint representations
  ☆16Updated 3 years ago
• maggiecrow / DEprior
  ☆15Updated 4 years ago