Alternatives and similar repositories for spatialexperiment-analysis:

Users that are interested in spatialexperiment-analysis are comparing it to the libraries listed below

• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆19Updated 2 years ago
• LTLA / batchelor
  Clone of the Bioconductor repository for the batchelor package.
  ☆16Updated 6 months ago
• MSingerLab / COMETSC
  COMET Single-Cell Marker Detection tool
  ☆31Updated 2 years ago
• BUStools / BUS_notebooks_R
  R vignettes for processing BUS format single-cell RNA-seq files
  ☆20Updated 4 years ago
• immunogenomics / singlecellmethods
  Collection of useful methods for single cell analysis
  ☆14Updated 4 months 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
• powellgenomicslab / DropletQC
  Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
  ☆34Updated 3 years ago
• skinnider / dismay
  Calculation of distance metrics for matrices
  ☆25Updated 5 years ago
• bioturing / signac
  An analytics package for single cell data
  ☆21Updated 2 years ago
• LTLA / scRNAseq
  Clone of the Bioconductor repository for the scRNAseq package.
  ☆24Updated 6 months ago
• oganm / homologene
  An r package that works as a wrapper to homologene
  ☆42Updated last year
• tengfei-emory / scBatch
  Batch Effect Correction of RNA-seq Data through Sample Distance Matrix Adjustment
  ☆17Updated 3 years ago
• cancerbits / DElegate
  Wrapper and helper functions to use bulk RNA-seq differential expression methods with single-cell data
  ☆18Updated 11 months ago
• MonashBioinformaticsPlatform / celaref
  ☆14Updated 5 years ago
• jgamache014 / snRNA-seq-workflow
  Human brain, >200,000 nuclei
  ☆24Updated 3 years ago
• Sun-lab / scRNAseq_pipelines
  pipelines to process scRNA-seq data
  ☆11Updated 4 years ago
• stephaniehicks / scBatchPaper
  Code used for the single-cell RNA-Seq batch effects paper
  ☆10Updated 7 years ago
• adoostparast / CellR
  CellR: single-cell RNA-Seq guided deconvolution of cellular composition from bulk-tissue RNA-Seq
  ☆15Updated 3 years ago
• LTLA / SingleCellThoughts
  Assorted thoughts, explanations and justifications for code in the scran package and the simpleSingleCell workflow.
  ☆44Updated 4 years ago
• stephaniehicks / methylCC
  R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms
  ☆19Updated 2 years ago
• Shians / CellBench
  R package for benchmarking single cell analysis methods
  ☆30Updated last year
• GabrielHoffman / dreamlet
  Perform differential expression analysis on multi-sample single cell datasets using linear mixed models
  ☆20Updated last month
• forrest-lab / scMatch
  scMatch: a single-cell gene expression profile annotation tool using reference datasets
  ☆21Updated 4 years ago
• hms-dbmi / scw
  HSCI/Catalyst Single-cell RNA-Seq Workshop
  ☆19Updated 5 years ago
• xgaoo / ClusterMap
  ClusterMap is an R package to analyze and compare two or more single cell expression datasets.
  ☆20Updated 2 years ago
• pachterlab / kite
  kallisto index tag extractor
  ☆20Updated 5 years ago
• hb-gitified / cellrangerRkit
  Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
  ☆19Updated 5 years ago
• PoolLab / generecovery
  ☆29Updated last year
• davemcg / scEiaD
  Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas
  ☆25Updated last year
• shenorrLabTRDF / cellAlign
  ☆38Updated 4 years ago