Alternatives and similar repositories for Stereopy

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

• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆230Updated last year
• STOmics / SAW
  ☆183Updated last year
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆436Updated 2 weeks ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆451Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆407Updated 5 months ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆308Updated last week
• IanevskiAleksandr / sc-type
  ☆285Updated last year
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆454Updated last year
• navinlabcode / copykat
  ☆269Updated 3 months ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆171Updated 3 years ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆415Updated 3 weeks ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆245Updated 3 weeks ago
• digitalcytometry / cytotrace2
  CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.
  ☆219Updated last month
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆375Updated 6 months ago
• Winnie09 / GPTCelltype
  ☆222Updated last year
• JianYang-Lab / gsMap
  Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.
  ☆194Updated last month
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆343Updated 11 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆413Updated last week
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆215Updated last year
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆265Updated 2 weeks ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆464Updated 8 months ago
• sunduanchen / Scissor
  Scissor package
  ☆250Updated last year
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆234Updated last week
• pwwang / scplotter
  scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy…
  ☆292Updated 2 weeks ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆208Updated 2 weeks ago
• Teichlab / cellphonedb
  ☆358Updated 4 years ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆180Updated 2 weeks ago
• YMa-lab / CARD
  ☆129Updated last year
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆153Updated 3 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆311Updated 3 years ago