Alternatives and similar repositories for pySCENIC

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

• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆456Updated 5 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆434Updated last year
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆463Updated last year
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆372Updated 7 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆415Updated 2 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆559Updated 2 weeks ago
• Teichlab / cellphonedb
  ☆356Updated 3 years ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆432Updated 8 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆483Updated 4 months ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆355Updated 5 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆441Updated last month
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆425Updated 5 months ago
• hbctraining / scRNA-seq
  ☆572Updated 4 years ago
• cole-trapnell-lab / monocle3
  ☆397Updated last month
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆536Updated last year
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆345Updated last week
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆720Updated last week
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆498Updated last month
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆395Updated this week
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆373Updated 6 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆418Updated 2 weeks ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆473Updated 2 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆426Updated last week
• IanevskiAleksandr / sc-type
  ☆271Updated 8 months ago
• hbctraining / Intro-to-scRNAseq
  ☆612Updated 3 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆387Updated 3 weeks ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆632Updated 6 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆219Updated last week
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆424Updated 5 months ago