Table of Contents

Introduction to Analysis of Genomic Data

Overview of Key JMP Platforms for Analysis of Wide Data

Organizing Data

Importing Data

Importing Basic Text Files

Importing VCF Files

Importing Series Matrix Files

Importing MTX Files

Importing Data from IDAT Files

Importing GBS Files

Importing HDF5 Files

Quality Control and Normalization

Sequencing Variants Discovery

Genetic Marker Analysis

Genetics Platforms

Verifying Marker Encoding

Imputing Missing Values in Genotype Data Sets

Generating Predictor Formulas for Marker Simulation

Specifying Trait Selection Criteria for Marker Simulation

Pattern and Structural Discovery

Statistical Modeling

Predictive Modeling

Case Studies

Gene Expression Analysis of Estradial-Responsive Genes in a Cell Line

Genetic Analysis of 6 Loblolly Pine Traits

Analysis Of Single Cell Sequencing Data