通过StationaryOT分析来计算 scr 细胞的命运概率最终发现scr 突变层细胞同时具有皮层和内皮层的特性。有意思的是, scr 突变层细胞在发育早期(分生区)主要是类似皮层,而成熟区的细胞呈现出内皮层的特性(图6-1)。 图6-1 scr 突变层细胞由皮层到内皮层的特性转变 为了在体内进一步对scRNA-seq得到的结论进行验证,作...
为填补决这一空缺,近日,加州大学洛杉矶分校(UCLA)的李婧翌团队在Nature Communications发表了题为scReadSim, a single-cell RNA-seq and ATAC-seq read simulator的文章。 在文章中,作者开发了模拟器scReadSim用于产生仿真的scRNA-seq和scATA...
However, none of the few existing read simulators aim to mimic real data. Here, the authors introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that works by mimicking real data.Yan, GuanaoSong, DongyuanLi, Jingyi JessicaNature Communications...
input includes a real scATAC-seq dataset’s BAM file, the corresponding reference genome, and optionally, users’ trustworthy peaks and non-peaks in the input BAM file; if users do not input trustworthy peaks and non-peaks, scReadSim provides two options; see the subsection “scReadSim for sc...
1. Why single-cell RNA-seq 在人类组织中,细胞类型、状态和相互作用的多样性令人难以置信。为了更好地了解这些组织和现有的细胞类型,单细胞RNA-seq(scRNA-seq)提供了在单个细胞水平上表达基因类型的视角。 Image credit: courtesy of Dr. Ayshwarya Subramanian ...
To overcome this challenge, the development of effective imputation methods has become crucial in the field of scRNA-seq data analysis. Here, we propose an imputation method based on robust and non-negative matrix factorization (scRNMF). Instead of other matrix fa...
(1) The scRCAT-seq read distribution; (2) Location of the motifs which were associated with real TSSs/TESs around the peaks; (3) Sequence motifs possibly resulting in false-positive TSS/TES, such as the internal priming sites (see “Methods”) (Supplementary Table1). We implemented four ...
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Understand how to bring in data from single-cell RNA-seq experiments Quality control set-up 1. Exploring the example dataset 在本次研讨会上,我们将使用单细胞RNA-seq数据集,该数据集是Kang等人(2017年)进行的一项较大研究的一部分。在本文中,作者提出了一种利用遗传变异(eQTL)来确定基因的计算算法。 每...
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