Alternatives and similar repositories for scvelo

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

• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆448Updated last year
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆562Updated 5 months ago
• Teichlab / cellphonedb
  ☆359Updated 3 years ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆596Updated 3 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆401Updated 10 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆366Updated 4 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆321Updated 2 years ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆436Updated 9 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆447Updated 5 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆486Updated 6 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆430Updated 3 weeks ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆431Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆393Updated 3 months ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆469Updated last year
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆409Updated 3 weeks ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆453Updated last year
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆229Updated this week
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆437Updated 9 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆420Updated last month
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆393Updated this week
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆497Updated last month
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆395Updated 2 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆394Updated 3 weeks ago
• IanevskiAleksandr / sc-type
  ☆277Updated last year
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆415Updated 4 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆512Updated last month
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆311Updated 5 years ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆355Updated this week
• cole-trapnell-lab / monocle3
  ☆423Updated 2 months ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆294Updated 4 months ago