Alternatives and similar repositories for spacexr:

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

• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆349Updated last week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆416Updated last year
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆268Updated last month
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆318Updated 8 months ago
• IanevskiAleksandr / sc-type
  ☆257Updated 4 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆377Updated 2 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆328Updated last week
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆280Updated last month
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆268Updated 2 years ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆526Updated last month
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆343Updated 2 months ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆196Updated 6 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆226Updated last year
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆197Updated last year
• drieslab / Giotto
  Spatial omics analysis toolbox
  ☆292Updated last week
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆370Updated 3 months ago
• Teichlab / cellphonedb
  ☆353Updated 3 years ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆207Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆315Updated last month
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆212Updated 2 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆407Updated 2 months ago
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆362Updated 4 months ago
• samuel-marsh / scCustomize
  R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆247Updated last week
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆226Updated this week
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆388Updated this week
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆206Updated this week
• cole-trapnell-lab / monocle3
  ☆375Updated 2 months ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆221Updated 3 months ago
• navinlabcode / copykat
  ☆228Updated 9 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆345Updated this week