Alternatives and similar repositories for SpatialFeatureExperiment

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

• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆47Updated 6 months ago
• drighelli / SpatialExperiment
  ☆71Updated 8 months ago
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆21Updated 3 years ago
• kevinrue / velociraptor
  Toolkit for Single-Cell Velocity
  ☆59Updated 6 months ago
• tidyomics / tidySingleCellExperiment
  Brings SingleCellExperiment objects to the tidyverse
  ☆37Updated 2 months ago
• oganm / homologene
  An r package that works as a wrapper to homologene
  ☆49Updated 2 years ago
• vitessce / vitessceR
  R API and htmlwidget for Vitessce
  ☆44Updated 5 months ago
• Sarah145 / CCPlotR
  An R package for visualising cell-cell interactions
  ☆46Updated last year
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆52Updated 2 years ago
• pachterlab / voyager
  From geospatial to spatial -omics
  ☆100Updated 2 months ago
• hansenlab / tricycle
  ☆27Updated 3 years ago
• wmacnair / SampleQC
  Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data
  ☆39Updated 3 years ago
• powellgenomicslab / DropletQC
  Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
  ☆41Updated 4 years ago
• pachterlab / concordexR
  Compute the neighborhood consolidation matrix and identify SHRs
  ☆13Updated 7 months ago
• ludvigla / semla
  ☆98Updated 4 months ago
• mojaveazure / loomR
  An R-based interface for loom files
  ☆67Updated 5 years ago
• niaid / dsb
  Normalize CITEseq Data
  ☆67Updated 2 months ago
• korsunskylab / rcna
  R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)
  ☆15Updated 2 years ago
• Nanostring-Biostats / GeomxTools
  Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.…
  ☆47Updated 4 months ago
• MangiolaLaboratory / HPCell
  Convert your single-cell/spatial analyses to parallel HPC/cloud workflows just using pipes in R
  ☆16Updated last year
• 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
• cancerbits / DElegate
  Wrapper and helper functions to use bulk RNA-seq differential expression methods with single-cell data
  ☆21Updated 2 years ago
• randel / MIND
  Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution
  ☆47Updated 2 years ago
• kevinblighe / scDataviz
  scDataviz: single cell dataviz and downstream analyses
  ☆66Updated 4 years ago
• GabrielHoffman / dreamlet
  Perform differential expression analysis on multi-sample single cell datasets using linear mixed models
  ☆29Updated last week
• gjhunt / dtangle
  Cell type deconvolution from high-throughput gene expression profiling experiments.
  ☆31Updated 4 years ago
• milescsmith / ReductionWrappers
  R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)
  ☆36Updated last year
• carmonalab / SignatuR
  A database of useful gene signatures for single-cell analysis
  ☆28Updated 8 months ago
• Shians / CellBench
  R package for benchmarking single cell analysis methods
  ☆32Updated 2 years ago
• shenorrLabTRDF / cellAlign
  ☆43Updated 5 years ago