Alternatives and similar repositories for spacexr

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

• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆326Updated 9 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆422Updated last year
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆355Updated last month
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆464Updated last month
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆363Updated last week
• IanevskiAleksandr / sc-type
  ☆262Updated 6 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆398Updated last month
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆412Updated last week
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆536Updated this week
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆273Updated this week
• navinlabcode / copykat
  ☆233Updated 10 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆349Updated 4 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆332Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆339Updated 2 months ago
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆374Updated 5 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆213Updated this week
• Teichlab / cellphonedb
  ☆355Updated 3 years ago
• cole-trapnell-lab / monocle3
  ☆380Updated 4 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆295Updated 4 years ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆419Updated 2 months ago
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆242Updated last week
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆227Updated 2 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆276Updated 2 years ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆203Updated 8 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆317Updated 2 years ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆212Updated last month
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆405Updated last month
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆289Updated 2 months ago
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆257Updated 2 weeks ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆224Updated 2 weeks ago