ATAC-seq(Assay for Transposase-Accessible Chromatin with high throughput sequencing) 是2013年由斯坦福大学William J. Greenleaf和Howard Y. Chang实验室开发的用于研究染色质可及性(通常也理解为染色质的开放性)的方法, 原理是通过转座酶Tn5容易结合在开放染色质的特性,然后对Tn5酶捕获到的DNA序列进行测序。 真核...
并以基因表达数据为参照,指出相比于各种经验统计指标,上述方法获得的标度方差(scaled variance)能更好地衡量每个位点表观调控信号的样本间异质性水平(图A) ;然后,在评估其统计显著性时,引入区域筛选(subset selection)和缩尾处理(winsorization)等手段来控制潜藏真阳性位点对参数估计的影响,显著改善了...
we could first sequence 10% of the loaded cells to evaluate data quality and subsequently sequence the remaining 90% if warranted. We then tested all three strategies head-to-head (Additional file1: Fig
Cellcano is also robust against the anchor selection procedure and batch effects in the data. Cellcano has several advantages and methodological features. First, Cellcano uses gene scores as input, which has many advantages compared to using bin or peak counts: (1) genes have a much smaller ...
publicly available ChIP-seq datasets can be integrated to improve the accuracy of footprinting. Incorporating known enhancer-promoter interactions from chromatin conformation data would also be helpful. With the surge of deep learning, it would require more work on feature construction and selection in ...
calling看成一种对高维基因组数据的数据降维（dimensionality reduction）或特征选取（feature selection）。
上述方法获得的标度方差(scaled variance)能更好地衡量每个位点表观调控信号的样本间异质性水平(图A) ;然后,在评估其统计显著性时,引入区域筛选(subset selection)和缩尾处理(winsorization)等手段来控制潜藏真阳性位点对参数估计的影响,显著改善了HVR识别的统计功效,实现对被比较样本间表观组异质性的完整统计刻画(图...
handk. The sample corresponding to SRR891270 was optimally transposed by Tn5, preloaded with sequencing adapters, while the sample resulting in SRR580802 was over-transposed. The other two datasets were resulted from sub-optimal transposition. Biased size selection could have occurred during library ...
We start with the peak-cell matrix, then perform peak selection, normalization, dimensionality reduction, clustering, and visualization. We also visualize regulatory activity at marker genes and compute differential peaks. Dataset sizes for single-cell genomics studies are increasing, presently reaching ...
such knowledge can be used to inform the selection of CREs for knock-out or transgenic experiments. In order to facilitate accurate reconstruction of CRE activities using scATAC-seq data, this article introduces a new statistical and analytical framework SCATE (Single-Cell ATAC-seq Signal Extraction...