aertslab / pySCENIC
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
☆467Updated 9 months ago
Alternatives and similar repositories for pySCENIC:
Users that are interested in pySCENIC are comparing it to the libraries listed below
- RNA Velocity generalized through dynamical modeling☆423Updated last month
- A package to help convert different single-cell data formats to each other☆401Updated 11 months ago
- NicheNet: predict active ligand-target links between interacting cells☆510Updated 4 months ago
- ☆350Updated 3 years ago
- An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.☆433Updated 8 months ago
- R package for detecting doublets in single-cell RNA sequencing data☆435Updated 8 months ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆358Updated 3 weeks ago
- Scanpy Tutorials.☆196Updated this week
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆433Updated 9 months ago
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆395Updated last week
- ☆360Updated 3 weeks ago
- A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…☆478Updated last week
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆336Updated last month
- Analysis Pipeline for Single Cell ATAC-seq☆309Updated last year
- A tool for semi-automatic cell type classification☆330Updated last month
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆305Updated 6 months ago
- Inferring CNV from Single-Cell RNA-Seq☆589Updated 2 months ago
- This is the alpha version of the CellOracle package☆329Updated 3 weeks ago
- A list of scRNA-seq analysis tools☆659Updated last month
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆281Updated 4 years ago
- An overview of algorithms for estimating pseudotime in single-cell RNA-seq data☆415Updated last month
- Collections of library structure and sequence of popular single cell genomic methods☆446Updated last month
- 10x Genomics Single Cell Analysis☆378Updated last month
- Benchmarking analysis of data integration tools☆325Updated 2 weeks ago
- A toolkit for single-cell immune profiling☆323Updated this week
- Community-provided extensions to Seurat☆319Updated 2 months ago
- Table of software for the analysis of single-cell RNA-seq data.☆312Updated this week
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆297Updated 5 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆545Updated 2 months ago
- R package for integrating and analyzing multiple single-cell datasets☆399Updated 2 weeks ago