Alternatives and similar repositories for spatialexperiment-analysis

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

• cancerbits / DElegate
  Wrapper and helper functions to use bulk RNA-seq differential expression methods with single-cell data
  ☆21Updated 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 2 years ago
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆21Updated 3 years ago
• gillislab / MetaMarkers
  Efficiently compute robust markers across single-cell datasets
  ☆11Updated 4 years ago
• BUStools / BUS_notebooks_R
  R vignettes for processing BUS format single-cell RNA-seq files
  ☆21Updated 5 years ago
• GabrielHoffman / dreamlet
  Perform differential expression analysis on multi-sample single cell datasets using linear mixed models
  ☆29Updated last week
• statOmics / zinbwaveZinger
  Integrating zingeR with ZINB-WaVE weights
  ☆26Updated 7 years ago
• DiseaseNeuroGenomics / dreamlet
  Perform differential expression analysis on cohort-scale single cell datasets using linear mixed models
  ☆21Updated last week
• adoostparast / CellR
  CellR: single-cell RNA-Seq guided deconvolution of cellular composition from bulk-tissue RNA-Seq
  ☆19Updated 4 years ago
• GabrielHoffman / dreamlet_analysis
  Analysis code and results for dreamlet
  ☆10Updated 6 months ago
• skinnider / dismay
  Calculation of distance metrics for matrices
  ☆26Updated 6 years ago
• elolab / multisubjectDSanalysis
  ☆17Updated 3 years ago
• kieranrcampbell / switchde
  Inference of switch-like differential expression along single-cell trajectories
  ☆22Updated 8 years ago
• Shians / CellBench
  R package for benchmarking single cell analysis methods
  ☆32Updated 2 years ago
• xgaoo / ClusterMap
  ClusterMap is an R package to analyze and compare two or more single cell expression datasets.
  ☆20Updated 3 years ago
• bioturing / signac
  An analytics package for single cell data
  ☆22Updated 3 years ago
• jgamache014 / snRNA-seq-workflow
  Human brain, >200,000 nuclei
  ☆23Updated 4 years ago
• shenorrLabTRDF / cellAlign
  ☆43Updated 5 years ago
• hansenlab / tricycle
  ☆27Updated 3 years ago
• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆47Updated 6 months ago
• LieberInstitute / 10xPilot_snRNAseq-human
  10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC
  ☆25Updated 3 years ago
• oganm / homologene
  An r package that works as a wrapper to homologene
  ☆49Updated 2 years ago
• GregorySchwartz / tooManyCellsR
  An R wrapper for too-many-cells, for clustering single cells and analyzing cell clade relationships with colorful visualizations.
  ☆26Updated 5 years ago
• Sun-lab / scRNAseq_pipelines
  pipelines to process scRNA-seq data
  ☆12Updated 5 years ago
• powellgenomicslab / DropletQC
  Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
  ☆41Updated 4 years ago
• randel / MIND
  Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution
  ☆47Updated 2 years ago
• BaderLab / scRNAseqWorkflow
  Brendan's skeleton scRNAseq workflow using scran, Seurat, and scClustViz
  ☆11Updated 5 years ago
• LTLA / batchelor
  Clone of the Bioconductor repository for the batchelor package.
  ☆18Updated 10 months ago
• MSingerLab / COMETSC
  COMET Single-Cell Marker Detection tool
  ☆32Updated 3 years ago
• hb-gitified / cellrangerRkit
  Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
  ☆19Updated 6 years ago