Alternatives and similar repositories for anndata

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

• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆51Updated last year
• scverse / anndataR
  AnnData interoperability in R
  ☆82Updated last week
• 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 10 months ago
• const-ae / lemur
  Latent Embedding Multivariate Regression
  ☆91Updated 7 months ago
• lorenzobonaguro / cyCONDOR
  Flow cytometry analysis workflow. The aim of this project is to provide an intuitive workflow for the analysis of high-dimensionality cyt…
  ☆19Updated this week
• saeyslab / FlowSOM
  Using self-organizing maps for visualization and interpretation of cytometry data
  ☆28Updated 3 months ago
• RMolania / TCGA_PanCancer_UnwantedVariation
  ☆47Updated last year
• oganm / homologene
  An r package that works as a wrapper to homologene
  ☆46Updated last year
• wmacnair / SampleQC
  Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data
  ☆37Updated 2 years ago
• kevinrue / velociraptor
  Toolkit for Single-Cell Velocity
  ☆56Updated 5 months ago
• korsunskylab / rcna
  R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)
  ☆15Updated last year
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆82Updated 3 weeks ago
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆52Updated 3 weeks ago
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆41Updated last month
• saezlab / mistyR
  Multiview Intercellular SpaTial modeling framework
  ☆59Updated 2 weeks ago
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆33Updated last month
• stemangiola / CuratedAtlasQueryR
  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
  ☆92Updated 6 months ago
• stemangiola / tidySingleCellExperiment
  Brings SingleCellExperiment objects to the tidyverse
  ☆36Updated 6 months ago
• saeyslab / CytoNorm
  R library to normalize cytometry data
  ☆37Updated 2 months ago
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆32Updated last year
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆70Updated 11 months ago
• shenorrLabTRDF / cellAlign
  ☆41Updated 4 years ago
• cansysbio / ConsensusTME
  ConsensusTME Gene Sets and R Script
  ☆39Updated last year
• kevinblighe / scDataviz
  scDataviz: single cell dataviz and downstream analyses
  ☆63Updated 3 years ago
• MarioniLab / StabMap
  Mosaic single cell data integration using non-overlapping features
  ☆37Updated 2 years ago
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆75Updated 3 years ago
• mojaveazure / loomR
  An R-based interface for loom files
  ☆66Updated 4 years ago
• CostaLab / CrossTalkeR
  R package to do the Ligand Receptor Analysis Visualization
  ☆43Updated this week
• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆44Updated 8 months ago
• ZJUFanLab / CellTalkDB
  A manually curated database of literature-supported ligand-receptor interactions in human and mouse
  ☆31Updated 11 months ago