Alternatives and similar repositories for SpatialExperiment

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

• pachterlab / SpatialFeatureExperiment
  Extension of SpatialExperiment with sf
  ☆55Updated last month
• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆45Updated 3 months ago
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆21Updated 2 years ago
• tidyomics / tidySingleCellExperiment
  Brings SingleCellExperiment objects to the tidyverse
  ☆36Updated this week
• vitessce / vitessceR
  R API and htmlwidget for Vitessce
  ☆43Updated 2 months ago
• pachterlab / concordexR
  Compute the neighborhood consolidation matrix and identify SHRs
  ☆13Updated 4 months ago
• korsunskylab / rcna
  R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)
  ☆15Updated 2 years ago
• kevinrue / velociraptor
  Toolkit for Single-Cell Velocity
  ☆59Updated 3 months ago
• milescsmith / ReductionWrappers
  R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)
  ☆36Updated 10 months ago
• ludvigla / semla
  ☆94Updated last month
• MangiolaLaboratory / HPCell
  Convert your single-cell/spatial analyses to parallel HPC/cloud workflows just using pipes in R
  ☆14Updated 10 months ago
• Sarah145 / CCPlotR
  An R package for visualising cell-cell interactions
  ☆43Updated last year
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆52Updated last year
• oganm / homologene
  An r package that works as a wrapper to homologene
  ☆46Updated last year
• Nanostring-Biostats / GeomxTools
  Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.…
  ☆45Updated last month
• satijalab / seurat-object
  ☆30Updated last week
• JEFworks-Lab / SEraster
  Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis
  ☆18Updated 6 months ago
• pachterlab / voyager
  From geospatial to spatial -omics
  ☆98Updated last month
• ImmuneDynamics / Spectre
  A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
  ☆64Updated last month
• saezlab / MOFAcell
  Code used for muti cellular factor analysis
  ☆14Updated last year
• dynverse / anndata
  Annotated multivariate observation data in R
  ☆50Updated 4 months ago
• LTLA / scRNAseq
  Clone of the Bioconductor repository for the scRNAseq package.
  ☆29Updated 2 weeks ago
• AllenInstitute / mfishtools
  Building Gene Sets and Mapping mFISH Data
  ☆16Updated 2 months ago
• Oshlack / speckle
  R package for specialised analysis of single cell data
  ☆39Updated 3 years ago
• Elisseeff-Lab / domino
  A software package for connecting cell level features in single cell RNA sequencing data with receptor ligand activity. Please be aware t…
  ☆17Updated 10 months ago
• BaderLab / Tempora
  Pathway-based trajectory inference method for time-series scRNAseq data
  ☆25Updated 4 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆38Updated 4 months ago
• SydneyBioX / scClassify
  Hierarchical classification of cells
  ☆26Updated last year
• kstreet13 / scry
  Collection of analysis methods for small count data generated by rafalab members (the methods, not the data).
  ☆21Updated last year
• gdagstn / borges
  Antique or modern atlas-like depictions of non-linear dimensionality reduction for single cell data
  ☆18Updated 4 months ago