外显子和内含子读数的相对丰度,代表拼接和未拼接的转录物,可以用来推断scRNA-seq实验中的时间动态。RNAvelocity和scVelo等工具可以推断每个基因在细胞采样时的表达量是增加还是减少。 Differential expression 差异表达(DE)对于scRNA-seq来说更具挑战性,因为不仅仅是比较每个基因的单一数值,而是可以比较表达水平的分布。另...
Current best practices in single-cell RNA-seq analysis: a tutorial. Mol Syst Biol. 2019;15(6):e8746. Published 2019 Jun 19. doi:10.15252/msb.20188746 5. Chen G, Ning B, Shi T. Single-Cell RNA-Seq Technologies and Related Computational Data Analysis. Front Genet. 2019;10:317. ...
在scRNA-seq数据通过一些列的预处理,质控以及标准化之后,后续分析步骤需要通过识别细胞间的基因表达差异来进行聚类, 分析不同细胞群的差异性。这就涉及到了单细胞RNA数据处理中的特征选择,降维以及如何使数据可视化。 数据降维的必要性 如果将单个细胞看作一个数据点,那么检测的基因数就是其对应的变量数,也就是我们...
2. Luecken MD, Theis FJ. Current best practices in single-cell RNA-seq analysis: a tutorial. Mol Syst Biol. 2019;15(6):e8746. Published 2019 Jun 19. doi:10.15252/msb.20188746 3. Stuart T, Butler A, Hoffman P, et al. Comprehensive Integration of Single-Cell Data. Cell. 2019;177(...
scRNA-seq聚类分析(一) 使用最大差异的基因跨条件整合细胞,以鉴定彼此最相似的细胞 clustering analysis: aligning cells across conditions 现在我们有了高质量的细胞,在将细胞聚类并确定不同的潜在细胞类型之前,我们需要执行一些步骤。我们的数据集包含来自两个不同条件(Control and Stimulated)的两个样本,因此整合这些...
Conclusions We developed scRNASequest, an end-to-end pipeline for single-cell RNA-seq data analysis, visualization, and publishing. The source code under MIT open-source license is provided at https://github.com/interactivereport/scRNASequest. We also prepared a bookdown tutorial for the ...
Single-cell RNA-seq data analysis workshop by the Harvard Chan Bioinformatics Core. Lessons - hands-on Introduction to single-cell RNA-seq analysis using Seurat/RStudio, starting from count matrices. Rockfeller University scRNAseq tutorial ASAP: Full pipeline on a project imported from the Human...
ELATUS enhances the detection of functional lncRNAs from scRNA-seq data, detecting their expression with higher concordance than standard methods with the ATAC-seq profiles in single-cell multiome data. Interestingly, the better results of ELATUS are due to its advanced performance with an inaccurate...
Atutorialfor multisample SCPA, comparing pathways across a scRNA-seq T cell pseudotime trajectory Atutorialof a systematic analysis of many cell types across multiple tissues Atutorialfor a systems level analysis of many cells types in disease (COVID-19) ...
Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological signals representing no or low gene expression, while others regard zeros as missing data to be corrected. To help address the controversy, here we discu