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In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and ... is a list of potential targets for each TF (and it can be applied to scRNA-seq. ... <看更多>
Gene regulatory network analysis in single cells - Sara Aibar - RegGen - ISMB/ECCB 2017. ... <看更多>
#1. SCENIC
SCENIC+ is a tool which takes combined single-cell crhomatin accessibility and gene expression data as input to infere enhancer-drive gene regulatory networks.
#2. SCENIC: single-cell regulatory network inference and clustering
SCENIC is a generally applicable method for the analysis of scRNA-seq data that exploits TFs and cis-regulatory sequences to guide the discovery ...
#3. SCENIC: Single-cell regulatory network inference and clustering
To evaluate the performance of SCENIC, we applied it to a scRNA-seq data set with well-known cell types from the adult mouse brain (Fig. 1b-e).
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data. scenic.aertslab.org. License. View license.
#5. SCENIC+: single-cell multiomic inference of enhancers and ...
SCENIC+ provides critical insight into gene regulation, starting from multiome atlases of scATAC-seq and scRNA-seq. The SCENIC+ suite is ...
#6. SCENIC (Single-Cell rEgulatory Network Inference and ...
SCENIC (Single-Cell rEgulatory Network Inference and Clustering) and Regulon Enrichment. GRN inference, scRNA-Seq, regulons, SCENIC, HPC.
#7. [scRNA-seq]单细胞转录因子分析——SCENIC实操示例
之前的文章我们写到了用SCENIC对单细胞RNA测序数据进行转录因子分析的原理：[scRNA-seq]单细胞转录因子分析——SCENIC算法简析。在这篇推送中，我们就用 ...
#8. Gene regulatory network inference with SCENIC reveals cell...
(A) Unbiased clustering in Seurat (left panel) is similar to regulon-based clustering in SCENIC (right panel) for the scRNA-Seq dataset, resulting in the ...
#9. Chapter 16 SCENIC | Single Cell Multi-Omics Data Analysis
16.1 Load Seurat Obj · 16.2 Filtering genes for calculating time · 16.3 Tranfer into loom files · 16.4 Run SCENIC vis pySCENIC · 16.5 Retrieve AUC scores per cell.
#10. Robustness and applicability of transcription factor and ...
SCENIC is a com- putational workflow that comprises the construction of gene regulatory networks (GRNs) from scRNA-seq data that are subsequently interrogated ...
#11. A scalable SCENIC workflow for single-cell ... - RNA-Seq Blog
SCENIC reconstructs regulons (i.e., transcription factors and their. ... and transfer learning for functional annotation of scRNA-seq data.
#12. pySCENIC — pySCENIC latest documentation
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists ...
#13. A scalable SCENIC workflow for single-cell gene ... - Lirias
SCENIC has been refactored and reimplemented in Python (pySCENIC), resulting in ... Peripheral Blood Mononuclear Cells dataset and a panel of scRNA-seq ...
#14. Revealing key regulators of neutrophil function during ... - PLOS
In the current study, we re-analysed published scRNA-seq datasets ... (C) SCENIC results for neutrophil transcriptional regulatory networks.
#15. Single-Cell Regulatory Network Inference and Clustering ...
Single-cell RNA sequencing (scRNA-seq) technology has been widely used ... Clustering of cells based on SCENIC regulon activity shows that ...
#16. Single-cell RNA-seq and chromatin accessibility profiling ...
(c) t-SNE plot embedding of all γδ T cells from scRNA-seq data, ... Single-cell regulatory network inference and clustering (SCENIC) ...
#17. aertslab/SCENIC: vignettes/SCENIC_Running.Rmd - RDRR.io
In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and ... is a list of potential targets for each TF (and it can be applied to scRNA-seq.
#18. A scalable SCENIC workflow for single-cell gene regulatory ...
SCENIC reconstructs regulons (i.e., transcription factors and their target genes) assesses the activity of these discovered regulons in individual cells and ...
#19. Functional inference of gene regulation using single-cell multi ...
apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting ... suggests that SCENIC-prioritized TF regulators tend to bind pro-.
#20. 单细胞转录因子分析之SCENIC流程 - 生信菜鸟团
... AUCell to identify cells with active gene sets (gene-network) in scRNA-seq data. 所以，实际上学习这个SCENIC流程，必须要先学习这3个R包的 ...
#21. SIGNET: single-cell RNA-seq-based gene regulatory network ...
The combination of regulatory sequence analysis with scRNA-seq data analysis ... SCENIC [9] combines a random forest model used to predict ...
#22. SCope - FLY CELL ATLAS
SCope is a fast, user-friendly visualization tool for large-scale scRNA-seq datasets, ... scenic-v2 - Data from: SCENIC+: single-cell multiomic inference of ...
#23. Role of Calcium Signaling Pathway-Related Gene Regulatory ...
Furthermore, SCENIC was used to identify transcription factors (TFs) regulating these core genes using scRNA-seq data.
#24. SCENIC: 单细胞RNA-seq数据推断基因调控网络和细胞功能聚类
作者拿成年小鼠大脑的已知细胞类型的scRNA-seq数据集来测试SCENIC，来评估其准确性。 分析了1,046个初始共表达模块中的151个Regulons，这些Regulons ...
#25. 以single-cell RNA-seq数据推断基因调控网络和细胞功能聚类
SCENIC 准确性评估. 作者拿成年小鼠大脑的已知细胞类型的scRNA-seq数据集来测试SCENIC，来评估其准确性。
#26. Single-Cell Regulatory Network Inference And Clustering - ORBi
To test SCENIC performances we applied it to a scRNA-seq data set with well-known cell types from the adult mouse brain previously described in ...
#27. Predicting gene regulatory networks from cell atlases
To infer GRNs, we applied SCENIC, a framework for network inference, reconstruction, and clustering from scRNA-seq data (10).
#28. SCENIC单细胞转录因子调控网络分析- 基因 - 搜狐
SCENIC 是一种重建基因调控网络（GRN）并从scRNA-seq数据中鉴定stable cell states的工具。基于共表达和DNA模基序（motif）分析推断基因调控网络，然后 ...
#29. Gene Regulatory Network in scverse - scRNA-seq
You don't have scATAC-seq data: In case you only have scRNA-seq the ... of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and ...
#30. Single-Cell Transcriptomics Reveals Core Regulatory ... - MDPI
Furthermore, we used Single-Cell rEgulatory Network Inference and Clustering (SCENIC) analysis on our scRNA-seq data to examine the gene regulatory networks ...
#31. Stein Aerts on Twitter: "To our dearest SCENIC users: we ...
A scalable SCENIC workflow for single-cell gene regulatory network ... In this study, scRNA-seq and scATAC-seq atlases of the Drosophila ...
#32. Single cell RNA-seq analysis
scRNA -seq data analysis ... SCENIC. • BEELINE. – Single cell deconvolution. • CIBERSORTx ... SingleR: Reference-based annotation of scRNA-seq.
#33. SCENIC: Single-cell regulatory network inference and clustering
We present SCENIC, a computational method for simultaneous gene ... for SINgle CEll RNA-seq profiling Analysis) for processing scRNA-seq ...
#34. FlyBase:ScRNA-Seq
SCENIC infers Gene Regulatory Networks and cell types from single-cell RNA-seq data. Aibar et al. Van de Sande et al. SCope, SCope is a fast ...
#35. Cell profiling of mouse acute kidney injury reveals ... - PNAS
Recent single cell RNA-seq (scRNA-seq) analyses have revealed unexpected ... We then utilized the SCENIC package to generate cell regulatory networks from ...
#36. Identification of genomic enhancers through spatial integration ...
20,000 UMIs and 10,000 fragments per cell for scRNA-seq and ... Next, we used SCENIC (Single-Cell rEgulatory Network Inference.
#37. AUCell - Bioconductor
“SCENIC: Single-Cell Regulatory Network Inference And Clustering.” Nature Methods, 14, 1083-1086. doi: 10.1038/nmeth.4463. Aibar S, Aerts S (2016). “AUCell.
#38. SCope - bio.tools
SCope is a fast visualization tool for large-scale and high dimensional scRNA-seq datasets. Currently the data format supported by SCope is .loom.
#39. scRNA-Seq数据分析之SCENIC分析—寻找细胞群体中的驱动基因
SCENIC 分析是对ScRNA-Seq数据中转录因子（Transcription Factors，TFs）进行研究，最终筛选得到调控强度显著、处于核心作用的TFs，结果通常以热图形式 ...
#40. Single-Cell Regulatory Network Inference and Clustering ...
clustering (SCENIC) analysis using scRNA-seq data set GSE147285. (A) Cell number for endothelial cells (ECs), endoneurial (Endo), ...
#41. SCENIC-R安装及运行 - 生信小木屋
SCENIC 的实现包括R版本和Python版本，本文参考SCENIC: Introduction and ... sets (gene-network) in scRNA-seq data（识别具有活性基因集的细胞）.
#42. Single cell gene regulatory networks in plants: Opportunities ...
The majority of single cell RNA-seq (scRNA-seq) studies in plants have ... Single-Cell Regulatory Network Inference and Clustering (SCENIC) ...
#43. A Bayesian inference transcription factor activity model for the ...
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful ... target genes identified by SCENIC and by BITFAM by focusing.
#44. Comparison of two similar datasets with SCENIC - BioStars
Should SCENIC be run individually and a comparison somehow made, or would it be best ... scrnaseq scRNA-Seq SCENIC GRN compare • 712 views.
#45. Inference of cell type-speci c gene regulatory networks on cell ...
sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using ... Ontogenet in cell type 3 is worse than SCENIC.
#46. SCENIC | 从单细胞数据推断基因调控网络和细胞类型- 陈同的博文
AUCell： 用于鉴定scRNA-seq数据中具有活性基因集（基因网络）的细胞. 运行SCENIC需要安装这些软件包以及一些额外的依赖包：
#47. Single-Cell Transcriptome Analysis Reveals the Importance of ...
From the SCENIC analysis, we obtained 269 regulons and the corresponding gene ... In RA, scRNA-seq has allowed researchers to identify synovial cell types ...
#48. Single-Cell RNA Sequencing to Dissect the Immunological ...
scRNA -seq data of cardiac immune cells isolated from ... sion between different cell clusters.12 SCENIC identified.
#49. Integrated single-cell transcriptomic analyses reveal that ...
Here, we analyzed various scRNA-seq data to discover a PN to MES cell ... in different tumor subsets were identified using SCENIC package.
#50. Gene regulatory network analysis in single cells - Sara Aibar
Gene regulatory network analysis in single cells - Sara Aibar - RegGen - ISMB/ECCB 2017.
#51. Unified single-cell analysis of testis gene regulation ... - eLife
We performed scRNA-seq to generate 25,423 cell profiles isolated from total testis ... but may yield similar results, as SCENIC.
#52. Robustness and applicability of functional genomics tools on ...
... pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq.
#53. Single-cell Gene Regulatory Network (scGRN) - NetBioLab
To overcome the high noise and sparsity of scRNA-seq data, SCENIC links cis-regulatory sequences to single-cell gene expression.
#54. scNetViz: Cytoscape networks for scRNA-seq analysis
Several ways of plotting the cells and gene expression data are also available. This app enables scientists who may not be experts in scRNA-seq ...
#55. Predicting gene regulatory networks from cell atlases
from scRNA-seq data (10). The SCENIC framework is applied directly on the single-cell expression matrix combining (i) “GRNBoost” for.
#56. Robustness and applicability of transcription ... - DSpace@MIT
With the advent of single-cell RNA sequencing (scRNA-seq), ... and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq.
#57. 理解して使うRNA Velocity解析ツール-最近のツール編
... 手法 (Dynamo, SCENIC+) の紹介https://qiita.com/masa12/items/ ... 利用し、細胞系統樹に分解されたscRNA-seqデータからvelocityフィールドを低 ...
#58. A scalable SCENIC workflow for single ... - Robrecht Cannoodt
How to perform a fast SCENIC analysis alongside standard best practices steps on single-cell RNA-sequencing data.
#59. RNA-Seq Analysis: Methods, Applications and Challenges
Theoretically, the cells of Qiu et al., 2017 monocle-release/ scRNA-seq can be ... SCENIC method to reconstruct the gene regulatory network from scRNA-seq ...
#60. Machine Learning and Mathematical Models for Single-Cell ...
The dataset is a portion of mouse scRNA-seq data measured by Microwell-Seq, ... methods: SCENIC (Single-cell regulatory network inference and clustering) ...
#61. Dynamics and Complexity of Molecular Networks Controlling ...
The corresponding auxiliary datasets used for SCENIC analysis are human cisTarget ... scRNA-seq is conducted at 3- and 7-days after transduction of shAPC or ...
#62. Developmental Models 2.0 - 第 78 頁 - Google 圖書結果
The DEGs of each cluster in scRNA-seq and the differentially accessible genes ... We predicted transcription factor regulons using SCENIC (Aibar et al., ...
#63. Advanced Perspectives in Cell Therapy and Correlated ...
We observed different SCENIC-predicted TFs expressed exclusively in ... which can be identified via scRNA-seq data analysis (Armingol et al., 2021).
#64. New Roles of Neutrophils and Granulocytic MDSC in Autoimmune ...
Default parameters were used for the SCENIC workflow in R and the normalized ... we performed analysis of a previously published scRNA-seq dataset ...
scenic scrna 在 aertslab/SCENIC - GitHub 的推薦與評價
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data. scenic.aertslab.org. License. View license. ... <看更多>