Alternatives and similar repositories for spacexr

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

• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆442Updated last year
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆371Updated last month
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆358Updated 2 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆380Updated last week
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆467Updated last month
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆433Updated 4 months ago
• IanevskiAleksandr / sc-type
  ☆274Updated 10 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆296Updated 2 years ago
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆261Updated 3 weeks ago
• Teichlab / cellphonedb
  ☆359Updated 3 years ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆238Updated this week
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆395Updated last month
• cole-trapnell-lab / monocle3
  ☆409Updated 2 weeks ago
• navinlabcode / copykat
  ☆254Updated last year
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆408Updated this week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆382Updated 8 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆421Updated last month
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆294Updated 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…
  ☆234Updated 8 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆349Updated this week
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆574Updated 2 months ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆289Updated last month
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆348Updated 10 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆431Updated 7 months ago
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆308Updated last year
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆213Updated last year
• quadbio / scRNAseq_analysis_vignette
  Tutorial for scRNA-seq data analysis beginners using R
  ☆221Updated 7 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆230Updated 2 years ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆434Updated last month
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆467Updated last year