Alternatives and similar repositories for anndataR

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

• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆51Updated last year
• const-ae / lemur
  Latent Embedding Multivariate Regression
  ☆90Updated 6 months ago
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆33Updated 11 months ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆81Updated 9 months ago
• pachterlab / voyager
  From geospatial to spatial -omics
  ☆93Updated 2 months ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 2 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆74Updated 2 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆82Updated 2 weeks ago
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆52Updated last month
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆68Updated 10 months ago
• dynverse / anndata
  Annotated multivariate observation data in R
  ☆47Updated last week
• Nanostring-Biostats / CosMx-Analysis-Scratch-Space
  This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…
  ☆67Updated last week
• wmacnair / psupertime
  psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
  ☆40Updated 2 years ago
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆33Updated 3 weeks ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆111Updated last month
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆75Updated last month
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated 11 months ago
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆52Updated 9 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆79Updated last week
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆65Updated 7 months ago
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆74Updated 2 years ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆73Updated 9 months ago
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆30Updated last year
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆71Updated last year
• BodenmillerGroup / imcRtools
  An R package for handling and analysing imaging mass cytometry data
  ☆26Updated last week
• KlugerLab / DAseq
  ☆41Updated 4 years ago
• saeyslab / FlowSOM
  Using self-organizing maps for visualization and interpretation of cytometry data
  ☆28Updated 2 months ago
• cellgeni / batchbench
  ☆46Updated 3 years ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆70Updated 2 years ago
• stemangiola / CuratedAtlasQueryR
  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
  ☆90Updated 5 months ago