Alternatives and similar repositories for pySCENIC:

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

• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆416Updated last year
• Teichlab / cellphonedb
  ☆353Updated 3 years ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆377Updated 2 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆526Updated last month
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆433Updated last month
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆438Updated 11 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆452Updated 2 weeks ago
• cole-trapnell-lab / monocle3
  ☆375Updated 2 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆343Updated 2 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆318Updated 8 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆482Updated 2 months ago
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆469Updated 10 months ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆601Updated 2 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆207Updated last week
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆314Updated last year
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆349Updated last week
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆328Updated 4 months ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆315Updated last month
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆559Updated 4 months ago
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆221Updated 2 years ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆407Updated 2 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆370Updated 3 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆292Updated 4 years ago
• IanevskiAleksandr / sc-type
  ☆257Updated 4 months ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆388Updated this week
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆420Updated 2 weeks ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆454Updated 3 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆395Updated 4 months ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆683Updated 3 weeks ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆328Updated this week