Alternatives and similar repositories for scanpy-tutorials

Users that are interested in scanpy-tutorials are comparing it to the libraries listed below

• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆398Updated 3 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆375Updated 7 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆381Updated last month
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆374Updated 7 months ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆283Updated 3 weeks ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆363Updated this week
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆287Updated last month
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆227Updated 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…
  ☆233Updated 7 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆435Updated last year
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆353Updated 3 weeks ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆419Updated 2 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆373Updated 2 months ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆263Updated 8 months ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆218Updated last week
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆391Updated last month
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆202Updated 6 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆292Updated last month
• IanevskiAleksandr / sc-type
  ☆274Updated 9 months ago
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆257Updated 2 months ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆221Updated 4 months ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆210Updated last year
• scverse / pertpy
  Single-cell perturbation analysis
  ☆198Updated this week
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆393Updated 4 months ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆245Updated last week
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆313Updated 6 months ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 4 years ago
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆213Updated 2 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆461Updated 6 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆237Updated this week