为了验证鉴定小鼠interneurons的Dlx1/2调控网络,作者分析了人脑的sNuc-Seq(Single nuclei RNA-Seq)数据集。 在人类脑sNuc-Seq数据集上,SCENIC也鉴定出由DLX1/2强烈驱动的interneurons细胞群,该群具有与小鼠相同的motif,并且识别出一组保守的靶标,包括DLX1本身。 接下来,作者将这种跨物种分析扩展到其他细胞类型。与基...
根据所用文库的制备方法,RNA序列((also referred to as reads or tags)将从转录本(10X Genomics, CEL-seq2, Drop-seq, inDrops)或全长转录本(Smart-seq)的3'端(或5'端)中衍生。 Image credit: Papalexi E and Satija R. Single-cell RNA sequencing to explore immune cell heterogeneity, Nature Reviews...
针对于初入门者的single-cell RNA-seq数据分析在线课程资料: Analysis of single cell RNA-seq datahemberg-lab.github.io/scRNA.seq.course/ 主讲人Vladimir Kiselev主编SC3和scmap两个single-cell RNA-seq数据分析包,其导师Martin Hemberg是剑桥教授。 有意思的是,现在R里处理single-cell RNA sequencing的package...
1.Falco,在cloud上 2.SCONE:single-cell RNA-seq data 质检和标准化的包 3.Seurat,R包 4.ASAP:(Automated Single-cell Analysis Pipeline,一个网络平台 而关于单细胞RNA-seq的局限主要来自: 1.扩增,每个cell分得的reads 2.细胞基因的特异性表达,以区分不同类的细胞 分析的流程图:...
[论文笔记] :MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions 论文是一种非参数方法将细胞分为不相交的细胞团,同时避免数据平滑 整个算法流程为: 1. 原始矩阵进行特征选择 2. 构建平衡KNN图:如果我们用传统的相似性网络作为基因的co-expr网络的时候,每个节点根据阈值的选择,不同...
theory based on the popular splicing analysis method rna velocity will also be demonstrated. finally, we will discuss our recent efforts to interpolate non-stationary time-series scrna-seq data using wasserstein-fisher-rao-metric unbala...
SinglecellRNA-seqdataanalysiswithR简介和实验设计质量控制数据预处理归一化和批处理效果校正数据集成ccamnn数据集对齐降维pcatsne和umap聚类差异基因表达分析细胞类型识别轨迹伪时间空间转录组学 SinglecellRNA-seqdataanalysiswithR CSC – IT科学中心是芬兰国家和高等教育机构拥有的芬兰信息技术专业中心。为高等教育机构,...
图1. TRUST4在整体RNA-seq数据上的应用 (a) TRUST4概览 (b) MiXCR、CATT、TRUST3和TRUST4从模拟RNA-seq数据中报告的TRB CDR3数量 (c) 以BCR-seq结果为金标准,六个整体RNA-seq样本的精确度和召回率 (d) 通过对SMART-seq数据进行分组创建的伪整体RNA-seq数据上,评估TRUST4和MiXCR组装的全长V、CDR3和J序...
Data Wrangling scRNAseq Identifying Cell Populations Feature Selection and Cluster Analysis Batch Effects Correcting Batch Effects Functional Analysis Pseudotime Cell Trajectories Functional Pseudotime Analysis Single Cell Multiomic Technologies CITE-seq and scATAC-seq 链接 那么,话不多说,上链接:/2019_scWorksho...
Single-cell RNA-seqTranscriptomicsSingle-cell RNA-sequencing technologies have revolutionized the way that researchers can interrogate cellular relationships and the level of detail by which tissue architecture can be characterized. Multiple cell capturing methods have been developed that, when coupled to ...