Alternatives and similar repositories for scvelo

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

• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆564Updated 6 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆450Updated last year
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆404Updated 11 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆367Updated 4 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆598Updated last month
• Teichlab / cellphonedb
  ☆359Updated 4 years ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆452Updated 6 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆321Updated 2 years ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆395Updated 4 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆411Updated last month
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆441Updated 10 months ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆441Updated this week
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆433Updated last week
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆396Updated 3 weeks ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆454Updated last year
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆487Updated 7 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆397Updated 3 months ago
• cole-trapnell-lab / monocle3
  ☆425Updated 3 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆420Updated last week
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆230Updated this week
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆473Updated last year
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆356Updated 2 weeks ago
• IanevskiAleksandr / sc-type
  ☆280Updated last year
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆421Updated 5 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆514Updated 9 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆403Updated 2 weeks ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆437Updated 2 weeks ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆294Updated 5 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆509Updated 2 months ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆301Updated this week