Alternatives and similar repositories for CellOracle

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

• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆393Updated last week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆425Updated last year
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆367Updated 3 weeks ago
• Teichlab / cellphonedb
  ☆355Updated 3 years ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆505Updated last year
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆357Updated 4 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆213Updated this week
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆329Updated 10 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆540Updated this week
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆365Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆341Updated 3 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆367Updated 2 weeks ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆468Updated 2 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆446Updated 3 months ago
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆259Updated 3 weeks ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆404Updated last month
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆409Updated 6 months 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…
  ☆224Updated 4 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆387Updated last month
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆333Updated this week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆208Updated 3 months ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆214Updated last month
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆276Updated last week
• IanevskiAleksandr / sc-type
  ☆265Updated 6 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆286Updated 2 weeks ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆197Updated 3 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆357Updated 2 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆421Updated 3 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆424Updated last week