SCENIC
Gene Network Inferrer
A tool for inferring Gene Regulatory Networks and cell types from single-cell RNA-seq data
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
420 stars
22 watching
95 forks
Language: HTML
last commit: 8 months ago
Linked from 1 awesome list
seandavi/awesome-single-cellRelated projects:
| Repository | Description | Stars |
|---|---|---|
| aertslab/cistopic | An R package for identifying cell states and cis-regulatory topics from single-cell epigenomics data | 135 |
 cabsel/sincerities | Infers gene regulatory networks from time-stamped single cell transcriptional expression profiles using a statistical method | 11 |
 pinellolab/dictys | Reconstructs dynamic gene regulatory networks from single-cell RNA and ATAC-seq data to understand cell-type specific transcription factor regulation. | 111 |
 buenrostrolab/figr | A computational framework that integrates single-cell chromatin accessibility and gene expression data to infer transcriptional regulators of target genes. | 36 |
| aertslab/scope | A tool for fast visualization of large-scale single-cell data | 68 |
 bimsbbioinfo/netsmooth | Improves single cell RNA-seq data by smoothing out noise using prior information from gene interaction networks | 27 |
 broadinstitute/tangram | A Python package for aligning single-cell transcriptomic data with spatial gene expression data. | 258 |
 catavallejos/basics | An integrated Bayesian hierarchical model to analyze single-cell sequencing data | 84 |
 inoue0426/drgat | This implementation uses Graph Attention Networks to predict drug response based on genetic influences in heterogeneous networks. | 3 |
 teichlab/spatialde | Tools and methods to analyze gene expression data in relation to spatial coordinates | 145 |
 qifeidkn/stagate | A software framework for learning spatial embeddings from high-dimensional transcriptomics data using an adaptive graph attention auto-encoder | 37 |
 gevaertlab/amaretto | An algorithm for identifying cancer driver genes by integrating multi-omics data and penalized regression | 16 |
 zjufanlab/spatalk | An R package that infers cell-cell communication and ligand-receptor-target networks from spatially resolved transcriptomic data | 62 |
 dmcable/spacexr | Software package for cell type identification and differential expression in spatial transcriptomics | 312 |
 fridleylab/spatialge | A software package for analyzing and visualizing spatial gene expression data from single-cell RNA sequencing assays. | 13 |