Analyze singlecell RNAsequencing data with JMP Genomics Meijian

What is JMP® Genomics? • Built on top of SAS and JMP • Analysis

Single-Cell RNA sequencing • Single-cell RNA sequencing (sc. RNA-Seq) examines the RNA from individual

Copyright © SAS Inst itute Inc. All rig hts reserved.

sc. RNA-Seq Data Analysis Challenges Sc. RNA-Seq data pose new challenges in visualization and

New Sc. RNA-seq Workflow • New sc. RNA-Seq Workflow performs standard exploration on sc.

What’s in the demo? • Classify cell populations in a PBMC data set •

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What is JMP® Genomics? • Built on top of SAS and JMP • Analysis tools and integrated workflows for: - Genomic data import and preprocessing - Next-Generation Sequencing data analysis - Differential expression pattern detection - Biomarker discovery - Crop, and livestock breeding Copyright © SAS Inst itute Inc. All rig hts reserved.

Single-Cell RNA sequencing • Single-cell RNA sequencing (sc. RNA-Seq) examines the RNA from individual cells with optimized next-generation sequencing (NGS) technologies • sc. RNA-Seq provides a higher resolution of cellular differences and a better understanding of the function of an individual cell in the context of its microenvironment • sc. RNA-Seq helps to uncover new and rare cell populations, track trajectories of distinct cell lineages in development, and reveal differentially expressed genes between specific cell types Copyright © SAS Inst itute Inc. All rig hts reserved.

sc. RNA-Seq Data Analysis Challenges Sc. RNA-Seq data pose new challenges in visualization and statistical analysis - High dimensionality - High sparsity - Varying heterogeneity across cell populations - Technical noise - Reproducibility Copyright © SAS Inst itute Inc. All rig hts reserved.

New Sc. RNA-seq Workflow • New sc. RNA-Seq Workflow performs standard exploration on sc. RNA-seq data set - sc. RNA-Seq data import & preprocessing - Variable gene selection methods - Sparse SVD analysis - Hierarchical Clustering - Feature Importance Screening - Differential Gene Expression - T-SNE and UMAP visualization (R required) - Dynamic Violin Plot Copyright © SAS Inst itute Inc. All rig hts reserved.