创建基因活性表达矩阵(gene activity matrix) 我们可以通过评估与基因相关的染色质区域的可及性来对基因组中的基因活性进行定量,并根据scATAC-seq数据创建一个新的gene活性表格,我们在这里仅采用一种简单的方法:sum统计与基因体和启动子区域重叠的fragement的个数 为了创建gene活性表达矩阵,我们提取每个gene的坐标并延长...
gene.activities<-GeneActivity(brain)# add the gene activity matrix to the Seurat objectasanewassaybrain[['RNA']]<-CreateAssayObject(counts=gene.activities)brain<-NormalizeData(object=brain,assay='RNA',normalization.method='LogNormalize',scale.factor=median(brain$nCount_RNA))DefaultAssay(brain)<-'...
# compute gene activities gene.activities <- GeneActivity(brain) # add the gene activity matrix to theSeuratobject as a new assay brain[['RNA']] <- CreateAssayObject(counts = gene.activities) brain <- NormalizeData( object = brain, assay = 'RNA', normalization.method = 'LogNormalize', ...
activities <- GeneActivity(brain) # add the gene activity matrix to the Seurat object as a new assay brain[['RNA']] <- CreateAssayObject(counts = gene.activities) brain <- NormalizeData( object = brain, assay = 'RNA', normalization.method = 'LogNormalize', scale.factor = median(brain...
(1)初始函数名为build_gene_activity_matrix。该函数接受一个inputCDS和一个Cicero连接列表,并输出一个非标准化的基因活动得分表。 注意: 输入的CDS必须在fData表中有一个名为“gene”的列,如果该peaks是一个启动子,则表示该基因,如果该...
gene activity matrix query = snap.pp.make_gene_matrix(adata, gff_file=gff_file) query.obs_names = adata.obs_names scRNA-seq数据 从网站下载的已经注释好的单细胞转录组h5ad文件作为reference reference = sc.read("10x-Multiome-Pbmc10k-RNA.h5ad") ...
ZZZ3 is required for ATAC complex-dependent gene expression To determine the functional importance of H3 recognition by the ZZ domain in cells, we first investigated its role in ZZZ3 binding to chromatin. We performed ChIP-seq experiments in H1299 cells to assess the genome-wide occupancy of ...
and used to construct and visualize derived features such as promoter-sums that pool together counts from peaks associated with a gene. Peaks are enriched for transcription factor (TF) binding motifs and the presence of certain motifs can be indicative of transcription factor activity. To identify ...
3. Tripodi IJ, Allen MA, Dowell RD. Detecting differential transcription factor activity from ATAC-seq data. Molecules. 2018 May;23(5).
1）Signac是通过 GeneActivity() 函数 https://satijalab.org/signac/reference/geneactivit 来实现的，默认参数是基因上游2kb到TES区域。 2）而ArchR是通过 addGeneScoreMatrix() 函数 https://www.archrproject.com/reference/addGeneScoreMatrix.html 来实现的（createArrowFiles函数也会用默认参数...