对于常规的ATAC-seq数据鉴定转录因子活性只用前三个选项即可完成。 1-ATACorrect ATAC-seq测序中用到的Tn5转座酶具有明显的的插入偏见,这干扰了足迹分析,因此应该进行校正。ATACorrect选项用来实现这种校正。 输入文件包括该样本ATAC-seq的bam文件,基因组序列文件、该样本ATAC-seq 鉴定到的peak的bed文件(可查看往期推送...
Benefiting from the accumulating chromatin accessibility data and deep learning advances, we developed a new computational method named DeepTFni to infer TRNs from the single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data. By implementing a graph neural network, ...
整体把握CHIP-seq图谱特征：peak/reads在基因组上的分布、peak在元件上的富集、peak在基因元件上的分布、...
据介绍,ATACdb是一个强大的平台,提供最全面的可访问的染色质数据、QC、转录因子足迹和各种其他注释。当前版本的ATACdb具有来自NCBI GEO/SRA数据库的1400多个ATAC-seq样本的52,078,883个区域。 Database content and construction Data-Browse 在Data-Browse(数据浏览)模块,可以根据样品的类型(组织、干细胞、细胞系、诱...
ATAC-Seq技术在间充质干细胞成脂分化早期研究中的应用
To explore the related functions of chromatin open state in clear cell renal carcinoma (ccRCC) using the assay for transposase accessible chromatin using sequencing (ATAC-seq) data and transcriptome sequencing (RNA-seq) from The Cancer Genome Atlas (TCGA) database. Peaks of ATAC-seq data were ...
scRNASeqDB- A database aggregating human single-cell RNA-seq datasets.ref ShinyCortex- a resource that brings together data from recent scRNA-seq studies of the developing cortex for further analysis. ShinyCortex is based in R and displays recently published scRNA-seq data from the human and mo...
(ii) looking at overlap between islet ATAC-seq data and putative TF binding motifs. TF binding motif analysis of ATAC-seq data was performed using HOMER v4.7.217. Only known motifs from HOMER’s motif database were considered. We studied motifs enriched in ATAC-seq peaks of non-diabetic ...
library(biovizBase) 3.2 读入注释文件 library(EnsDb.Hsapiens.v86) annotation <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86) seqlevelsStyle(annotation) <- 'UCSC' blacklist <- blacklist_hg38 3.3 读入数据 counts <- Read10X_h5("/ATAC/fastq/pbmc_3k/outs/filtered_feature_bc_matrix.h5") ...
使用Signac包进行单细胞ATAC-seq数据分析(二):Motif analysis with Signac Davey1220关注IP属地: 广东 0.1512020.04.29 08:14:02字数671阅读6,161 在本教程中,我们将学习使用Signac包进行DNA序列的motif富集分析。Signac包可以使用两种互补的方法进行motif分析:一种是通过在一组差异可及性peaks中找到overrepresented的...