Computational Systems Biology Methods and Protocols.7z

due to their short reads. Using the human genome GRCh38 as reference, 57,992 annotated genes can be used to produce the gene exp ...

Feature reduction is performed often using two criteria. The first one is to remove genes with non-zero read counts in less than ...

5 Cluster Analysis Currently, the clustering methods in the scRNA-seq data analysis are actually using dimension reduction metho ...

smooth measure of the effective number of neighbors. The perfor- mance of t-SNE is fairly robust to changes in the perplexity an ...

on the clustering results. Cluster analysis is also used to identify cell states, particularly their stages of the cell cycle. T ...

produce high-depth data and using the software Fastq_clean to clean raw sequenced data with quality control. The software STAR [ ...

Acknowledgments I appreciate help equally from the people listed below. They are Professor Wenjun Bu; Professor Lin Liu; Ph.D. s ...

Levina E, Bickel PJ (2004) Maximum likeli- hood estimation of intrinsic dimension. Adv Neural Inf Proces Syst 17:777–784 Camast ...

Chapter 19 Applications of Single-Cell Sequencing for Multiomics Yungang Xu and Xiaobo Zhou Abstract Single-cell sequencing inte ...

acid extraction and amplification, sequencing library preparation, and sequencing and bioinformatic data analysis (Fig.1). 1.1 S ...

1.1.1 Flow Cytometry Among the various types of flow cytometers, the fluorescence- activated cell sorting (FACS) systems provide ...

acid amplification in nanoliter volumes (Fig.2B). Once captured, cells can be visualized on the chip, confirming the presence of ...

important research field. Particularly, the access to cells in situ is of interest [22]. In combination with immune histological ...

1.3 Sequencing Genomes of Single Cells Although bulk approaches for studying genetic variation have iden- tified thousands of ne ...

representation bisulfite sequencing (scRRBS-seq) [52]. The second one, post-bisulfite adaptor tagging (PBAT) [53], was implement ...

used. The first development of single-cell Hi-C used manual sepa- ration and labeling of amplified ligation products from single ...

computationally investigates both the DNA methylation and copy number states from scRRBS sequencing libraries and in parallel me ...

experiments for read alignment, transcript quantification, quality control, normalization, and downstream modeling. For some of ...

Table 1Computational tools for multistep analyses of scRNA-seq dataTool Description Requirements Type Interface Operatingsystem ...

Table 1(continued)Tool Description Requirements Type Interface Operatingsystem Programinglanguages References NormalizationSingl ...