Alternatives and similar repositories for cellrank:

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

• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆320Updated 9 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆344Updated 3 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆360Updated last month
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆213Updated this week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆203Updated 2 months ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆326Updated last month
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆364Updated 5 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆418Updated last year
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆288Updated 11 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆346Updated 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.
  ☆380Updated 3 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆434Updated last month
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆532Updated last week
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆348Updated 2 weeks ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆496Updated last year
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆197Updated last month
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆269Updated last week
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆352Updated 10 months ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆355Updated 3 weeks ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆231Updated last month
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆226Updated last year
• Teichlab / cellphonedb
  ☆353Updated 3 years ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆199Updated 8 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆329Updated 3 weeks ago
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆190Updated this week
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆216Updated 2 months ago
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆447Updated 3 months ago
• cole-trapnell-lab / monocle3
  ☆377Updated 3 months ago
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆218Updated 10 months ago
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆217Updated 9 months ago