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 last year
• NBISweden / single-cell_sib_scilifelab
  SIB/Scilifelab autumn school in single cell omics 2019.
  ☆22Updated 5 years ago
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆28Updated last year
• JinmiaoChenLab / FastIntegration
  FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis
  ☆23Updated 4 months ago
• davemcg / scEiaD
  Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas
  ☆25Updated last year
• broadinstitute / single_cell_classification
  Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
  ☆29Updated 4 years ago
• adoostparast / CellR
  CellR: single-cell RNA-Seq guided deconvolution of cellular composition from bulk-tissue RNA-Seq
  ☆17Updated 3 years ago
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆40Updated 2 weeks 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
• UPSUTER / GEMLI
  ☆30Updated last month
• ZJUFanLab / CellTalkDB
  A manually curated database of literature-supported ligand-receptor interactions in human and mouse
  ☆29Updated 8 months ago
• Vivianstats / scINSIGHT
  Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data
  ☆21Updated 11 months 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
• wmacnair / psupertime
  psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
  ☆38Updated 2 years ago
• hsmaan / Iniquitate
  Analysis of imbalanced data and its impacts in a scRNA-seq integration setting
  ☆30Updated 2 weeks ago
• Jiaxin-Fan / MuSiC2
  cell type deconvolution for multi-condition bulk RNA-seq data
  ☆23Updated 3 years ago
• GregorySchwartz / tooManyCellsR
  An R wrapper for too-many-cells, for clustering single cells and analyzing cell clade relationships with colorful visualizations.
  ☆25Updated 5 years ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆26Updated 3 months ago
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆34Updated 3 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆31Updated 3 weeks ago
• gofflab / developing_mouse_retina_scRNASeq
  10x single cell RNA-seq data from the developing mouse retina
  ☆16Updated 4 years ago
• quadbio / simspec
  Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)
  ☆31Updated last year
• plger / pipeComp
  A R framework for pipeline benchmarking, with application to single-cell RNAseq
  ☆41Updated 3 years ago
• MarioniLab / StabMap
  Mosaic single cell data integration using non-overlapping features
  ☆37Updated 2 years ago
• broadinstitute / gtex-single-nucleus-reference
  Code repository for the snRNA-seq cross-tissue atlas project
  ☆20Updated 3 years ago
• cellatlas / cellatlas
  ☆16Updated 8 months ago
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆33Updated last month
• shenorrLabTRDF / bseqsc
  Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
  ☆45Updated last year