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
  ☆363Updated this week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆349Updated 4 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆348Updated 3 months ago
• 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
  ☆420Updated last year
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆219Updated 3 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆386Updated 4 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆363Updated 11 months ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆211Updated last month
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆203Updated 7 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆227Updated 2 years ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆500Updated last year
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆354Updated last month
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆257Updated last week
• Teichlab / cellphonedb
  ☆354Updated 3 years ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆317Updated 2 years ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆363Updated 2 months ago
• IanevskiAleksandr / sc-type
  ☆262Updated 6 months ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆271Updated last month
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆199Updated last year
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆438Updated 2 months ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆334Updated 2 months ago
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆305Updated 2 weeks ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆280Updated last year
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆535Updated 2 weeks ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆197Updated 2 months ago
• cellgeni / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆135Updated 2 years ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆205Updated 3 months ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆157Updated 2 years ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆249Updated 5 months ago