Alternatives and similar repositories for ideas:

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

• gambalab / gficf
  An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization
  ☆18Updated last year
• PoolLab / generecovery
  ☆29Updated 2 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆31Updated 2 months ago
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆49Updated this week
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated 2 years ago
• AmandaKedaigle / OrganoidAtlas
  Code to go along with https://doi.org/10.1016/j.cell.2022.09.010
  ☆20Updated 3 years ago
• BradBalderson / Cytocipher
  Analysis methods for analysing single cell RNA-seq data; particularly with the goal of checking if tentative clusters of cells are signif…
  ☆37Updated last year
• neurorestore / DE-analysis
  ☆37Updated 3 years ago
• UPSUTER / GEMLI
  ☆30Updated 3 months ago
• NBISweden / single-cell_sib_scilifelab
  SIB/Scilifelab autumn school in single cell omics 2019.
  ☆22Updated 5 years ago
• broadinstitute / single_cell_classification
  Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
  ☆29Updated 5 years ago
• Jiaxin-Fan / MuSiC2
  cell type deconvolution for multi-condition bulk RNA-seq data
  ☆25Updated 3 years ago
• JinmiaoChenLab / FastIntegration
  FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis
  ☆23Updated 6 months ago
• netbiolab / scHumanNet
  Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3
  ☆42Updated last year
• sqjin / CellChatShiny
  Standalone shiny server container for viewing CellChat object
  ☆12Updated 4 years ago
• wenweixiong / MARVEL
  ☆49Updated 9 months ago
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆29Updated last year
• hsmaan / Iniquitate
  Analysis of imbalanced data and its impacts in a scRNA-seq integration setting
  ☆30Updated last month
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated 4 months ago
• JCVenterInstitute / FRmatch
  Cell type matching in single-cell RNA-sequencing data using FR-Match
  ☆19Updated last month
• aertslab / GENIE3
  GENIE3 (GEne Network Inference with Ensemble of trees) R-package
  ☆30Updated 3 years ago
• edroaldo / fusca
  Framework for Unified Single-Cell Analysis (FUSCA) is a software package for single-cell data analysis developed in R. At the moment, it …
  ☆19Updated 2 years ago
• RMolania / TCGA_PanCancer_UnwantedVariation
  ☆47Updated last year
• lcmmichielsen / scHPL
  ☆35Updated 2 months ago
• jfnavarro / st_analysis
  A toolset for analysis and visualisation of Spatial Transcriptomics datasets.
  ☆18Updated 3 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆59Updated 2 years ago
• cellatlas / cellatlas
  ☆16Updated 9 months ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆40Updated 3 months ago
• wmacnair / psupertime
  psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
  ☆39Updated 2 years ago
• PoolLab / ReferenceEnhancer
  ☆20Updated last year