Alternatives and similar repositories for celltypist

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

• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆220Updated this week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆378Updated 8 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆438Updated last year
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆367Updated 3 weeks ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆285Updated 2 weeks ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆377Updated 2 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆427Updated 3 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆394Updated last month
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆376Updated 2 weeks ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆295Updated 2 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆354Updated last month
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆382Updated 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
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆464Updated 6 months ago
• IanevskiAleksandr / sc-type
  ☆275Updated 10 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆440Updated 9 months ago
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆258Updated 2 months ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆228Updated 2 months ago
• Winnie09 / GPTCelltype
  ☆207Updated last year
• Teichlab / cellphonedb
  ☆357Updated 3 years ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆566Updated last month
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆237Updated this week
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆314Updated 6 months ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆289Updated 2 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
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated 6 months ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆538Updated 2 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆393Updated last week
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆263Updated 9 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆345Updated this week