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.
☆444Updated 7 months ago
Related projects ⓘ
Alternatives and complementary repositories for pySCENIC
- RNA Velocity generalized through dynamical modeling☆418Updated last month
- ☆345Updated 2 years ago
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆335Updated last month
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆421Updated 7 months ago
- NicheNet: predict active ligand-target links between interacting cells☆489Updated 2 months ago
- R package for detecting doublets in single-cell RNA sequencing data☆416Updated 6 months ago
- ☆344Updated 2 weeks ago
- A package to help convert different single-cell data formats to each other☆383Updated 8 months ago
- This is the alpha version of the CellOracle package☆313Updated last week
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆387Updated last week
- Collections of library structure and sequence of popular single cell genomic methods☆437Updated 2 weeks ago
- Analysis Pipeline for Single Cell ATAC-seq☆307Updated last year
- An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.☆395Updated 6 months ago
- Scanpy Tutorials.☆188Updated this week
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆293Updated last month
- Table of software for the analysis of single-cell RNA-seq data.☆309Updated this week
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆276Updated 2 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆297Updated 4 months ago
- Benchmarking analysis of data integration tools☆309Updated last month
- A tool for semi-automatic cell type classification☆302Updated 5 months ago
- Inferring CNV from Single-Cell RNA-Seq☆570Updated this week
- A toolkit for single-cell immune profiling☆310Updated this week
- R package for integrating and analyzing multiple single-cell datasets☆391Updated last week
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆274Updated 4 years ago
- Community-provided extensions to Seurat☆305Updated this week
- Reference mapping for single-cell genomics☆335Updated 3 weeks ago
- A list of scRNA-seq analysis tools☆635Updated this week
- High dimensional weighted gene co-expression network analysis☆360Updated last month
- A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…☆459Updated 2 weeks ago
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆218Updated last year