Alternatives and similar repositories for SpatialExperimentIO

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

• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆33Updated last month
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆33Updated 2 months ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆37Updated last month
• saezlab / MOFAcellulaR
  R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)
  ☆11Updated last year
• scverse / anndataR
  AnnData interoperability in R
  ☆84Updated this week
• damienArnol / svca
  ☆13Updated 6 years ago
• wanglab-broad / CAST
  CAST package
  ☆40Updated 8 months ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 6 months ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆23Updated 11 months ago
• bhuvad / SpaNorm
  R package for normalisation of spatial transcriptomics data
  ☆12Updated 3 weeks ago
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆77Updated 3 years ago
• nf-core / spatialxe
  ☆19Updated last week
• vitessce / vitessceR
  R API and htmlwidget for Vitessce
  ☆41Updated 9 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆38Updated last week
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆25Updated 2 years ago
• Teichlab / sctk
  ☆39Updated 9 months ago
• Sanofi-Public / spatialone-pipeline
  Spatial One
  ☆28Updated 8 months ago
• Teichlab / visium_stitcher
  Stitch multiple Visium slides together
  ☆16Updated last year
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆51Updated last year
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆53Updated last month
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆61Updated last week
• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆14Updated 3 years ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 3 weeks ago
• satijalab / panhumanpy
  ☆17Updated 2 months ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆27Updated 11 months ago
• dynverse / anndata
  Annotated multivariate observation data in R
  ☆48Updated last month
• korsunskylab / rcna
  R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)
  ☆15Updated last year
• BodenmillerGroup / imcRtools
  An R package for handling and analysing imaging mass cytometry data
  ☆27Updated last week
• JEFworks-Lab / veloviz
  RNA-velocity informed embeddings for visualizing cellular trajectories
  ☆43Updated 2 years ago
• const-ae / lemur
  Latent Embedding Multivariate Regression
  ☆92Updated 7 months ago