Workflows Accession Number Variable Add Fold Change Filter to Select Significant Tests Add Marker Genes to Explore Add Mean Difference Filter to select significant tests Additional Bandwidth on Each Side of Tracks Additional Fixed Effects Additional Random Effects Adjust Variability for these Random Effects Adjustment Effects Adjust Model with Additional Fixed Effects Allele Characters for A (P1 line) and B (P2 line) Alpha Alpha value for Beta distribution Annotation Analysis Group Variable to Use Annotation Analysis Group Variable Annotation Analysis Group Variable for Collapsing Rare Variants Annotation Analysis Group (Gene e.g.) Variable Annotation Chromosome Variable Annotation Group Variable Annotation Input SAS Data Set Annotation Label Variable Annotation Location Variable Annotation Merge Variables Annotation Plotting Group Variable Annotation Position Variable Annotation SAS Data Set Apply a Shifted log2 Transformation for QC Analysis Association Tests Automated Linkage Group Clustering Method Bandwidth Beta value for Beta distribution Binary Trait Variable Binary Trait Variables Break linkage groups based on: Break linkage groups between markers with large ordered distances By Variables Calculate trend odds ratios Categorical Variables Categorical Variables Defining Groups Categorical Variables for Model Cells with Maximum Features Detected Cells with Minimum Features Detected Censor Values Censor Variable Center columns Center rows Change Output Folder to Workflow Folder in settings moved to right panel Chromosome Variable Class Variables Cluster significant LSMean profiles Cluster significant Mean profiles Cluster Significant Results Clustering Method Collapse rare variants within analysis group Color Theme Color Variable Color Variable Type Color Variables Compress the K matrix Compression Rate Compute Q Variables from PCA Compute results for annotated rows only Compute results for exon annotated rows only Compute sandwich (empirical) estimator of covariance matrix Control Levels for Difference Comparisons Control Levels for Differential Expression Comparisons Conversion for P-Values Correlation and Grouped Scatterplots Correlation and Principal Variance Components Analysis Create add-in package Cross Type Cumulative Proportion of Variation to Explain with Principal Components Current Study Data Set Containing LSMeans Differences to Include Data Set of Differences to Include from Comparison Set Define linkage groups based on the: Delete rows: Delete rows with Interquartile Range satisfying this expression Delete rows with Mean satisfying this expression Delete rows with Median satisfying this expression Delete rows with Number of Missing Values satisfying this expression Delete rows with Percentile satisfying this expression Delete rows with Standard Deviation satisfying this expression Denominator Degrees of Freedom Method Direction of the Cutoff Direction of the Fold Change Cutoff Direction of the Mean Difference Cutoff Display marker genotype cell color plots Display principal components plots Distribution Analysis Estimate LSMeans for these Fixed Effects Event Trait Value Exon (Probeset) ID Variable Exon Annotation Chromosome Variable Exon Annotation Label Variable Exon Annotation Merge Variables Exon Annotation Position Variable Exon Annotation SAS Data Set Exon Annotation Transcript Variable Expected Segregation Ratios for AA AB BB Experimental Design SAS Data Set Features Detected in Minimum Cells File Containing Estimate Statements Filter Data with Zero or Missing Values Filter Rows Whose Proportion of Zero/Missing Values Exceeds this Cutoff Filter to Include Data in Analysis Filter to Include Exon Annotation Rows for ANOVA Filter to Include Individuals Filter to Include Markers Filter to Include miRNA Annotation Rows Filter to Include Observations Filter to Include Transcript Annotation Rows for ANOVA Filter to Select Markers for Computing the K Matrix Filter to Select Markers for PCA Fix covariance parameters Fixed Effects Fixed Effects for Differential Expression Fixed Effect Interactions with Exon ID Variable (Alternative Splicing) Fold Change Filter Cutoff Folder of Available Processes Folder of Available Settings Folder of Track Settings Files Format of Marker Variables Framework Linkage Group Variable Framework Map Data Set Framework Marker Name Variable Framework Order Variable GenBank Accession Variable Gene Description Variable Gene Length Variable Gene ID Variable Gene Symbol Variable Genes of Interest Genetic Distance Break Value Genotype Delimiter Genotyping Generation (n) Group Percentage for Deletion Grouping Method Grouping Recombination Fraction Threshold Hierarchical Clustering Hotellingâ€™s T-squared Test ID Variables Include 3D plots Include adjusted p-values in addition to -log10(p-values) Include Fold Changes in Addition to log Fold Changes Include fold changes in addition to log2 fold changes Include input data in package Include p-values in addition to -log10(p-values) Include study data in package Individuals Minimum Proportion of Nonmissing Genotypes Input data is log-transformed Input Genotype SAS Data Set Input SAS Data Set Intensity Columns to Filter Interaction Effects JMP Journal Output File K-Means Clustering Kernel Function Label Variable Launch ANOVA for Differential Expression Analysis Launch ANOVA Interface List every model fit List-Style Specification of Intensity Columns to Filter List-Style Specification of Marker Variables List-Style Specification of Trait Variables List-Style Specification of Variables Whose Rows are to be Clustered -log10(p-value) Cutoff LSMeans Control Levels LSMeans Difference Set for Volcano Plots MAF Threshold for Rare Variants Map Function Marker Name Variable Marker Variables Max Iteration of t-SNE Maximum Dimension of K Matrix Maximum Dispersion to Filter Genes Maximum Mean to Filter Genes Maximum Number of Chromosomes Per Row in 3D Display Maximum Number of Clusters for K-Means Maximum Number of Principal Components Maximum Number of Principal Components to Model Mean Difference Filter Cutoff Means Control Levels Means Difference Set for Volcano Plots Method Minimum Dimension of K Matrix Minimum Dispersion to Filter Genes Minimum Distance of UMAP Minimum Mean to Filter Genes Minimum Number of Clusters for K-Means Minimum Number of Observations Required for a Branch Minimum Proportion of Nonmissing Genotypes Minimum X Chromosome Heterozygosity for Females Minor allele frequency at Marker Locus Minor Allele Frequency Threshold Minor Allele Frequency Threshold for Including SNPs miRNA ID Variable Model interactions of these Fixed Effects with the Exon ID Variable (Screen for possible alternative splicing) Model Data As: Modeling Distribution Model these Fixed Effects Multiple-Locus Regression Model Multiple-Locus Radial Basis Machine (Kernel Method) Multiple Testing Correction Multiple Testing Method Multiple Testing Method for Segregation Tests Normalization Method Number of Clusters Number of Clusters Expected Number of Epochs of UMAP Number of Linkage Groups Number of Markers in Each Group Number of Neighbors of UMAP Number of Principal Components Number of Principal Components to Use Number of Rows in Input Data for Testing Run Number of SNPs to Test Number of the First Principal Component to Model Number of Variable Genes to Keep Analyze rare variants only Organism Output Data Set Output Data Set Containing Filtered Data Output Dimension of Embedding Output File Prefix Output Folder Output genotype LS means and diffs Output residuals from every model P-Value Adjustment p-Value Cutoff for Plots p-Value Cutoff for Segregation Test Plots PARMS Statement Values and/or Options PC Regression Model Pedigree ID Percentage of Mitochondria Genes Allowed Percentile to Compute for PCTL Statistic Perform Case-Control Association Tests Perform Missing Genotype by Trait Analysis Perform multiallelic analysis on multiallelic markers Perform shifted log2 transformation: Perplexity of t-SNE Plot Markers with significant p-values only Position Variable Prefix of Marker Genotype Variables Principal Component Analysis Principal Variance Component Effects for QC PROC GLIMMIX Estimation Method Random Effects Random Mating Generation (t) Prior to Inbreeding Random Statement Options Recode genotypes numerically (2,1,0) Recombination Fraction Break Value Recombination Fraction Cutoff Reference Trait Value Remove Mitochondrial Genes from Analysis Remove Ribosomal Genes from Analysis Replace Cluster Means with representative observations Replace highest values Replace intensities falling above this column percentile Replace intensities falling above this value Replace intensities falling at least this many standard deviations above the column mean Replace intensities falling at least this many standard deviations below the column mean Replace intensities falling below this column percentile Replace intensities falling below this value Replace lowest values Report SNP x Interaction Effect tests only Results to Include in the Review Review Output File Run Analyses Above... Run QC analyses: Run Subset and Reorder Genetic Data process to order marker data for QTL analysis Run t-SNE and UMAP (Appropriate R Packages Required) Scale columns Scale rows Select Comparison Set for Differential Expression Tests Select Comparison Set for Mean Differences Tests Select Method Separate and journal results by chromosome Sequence Kernel Association Test (SKAT) Server Output Directory Shifted log2 Transformation for ANOVA Shifted log2 Transformation for QC Shifting Factor Shifting Factor of log2 Transform for QC Shifting Factor of log2 Transform before Normalization or ANOVA Show Only: Single-Locus Genotype Tests Pearson chi-square and Fisherâ€™s exact Single-Locus Regression Model SNP ID Variable SNPs: Minimum HWE p-Value SNPs Minimum Minor Allele Frequency SNPs Minimum Missing Genotype by Trait p-Value SNPs Minimum Proportion of Nonmissing Genotypes Sort settings by: Strata Variables Study Study Name Study Output Folder Tau Value for TPM Template Study Template Study Output Folder Terminate further processes when an error occurs Test on a subset of SNPs Track Settings Files Trait Value of Individuals to Include in HWE Test Trait Variables Transcript Annotation Chromosome Variable Transcript Annotation Label Variable Transcript Annotation Merge Variables Transcript Annotation Position Variable Transcript Annotation SAS Data Set Transcript Annotation Variables to Keep Transcript Cluster ID Variable Two Way Clustering Type of Trait Use lower boundary constraint of 0 for K matrix covariance parameter Use QTL data numeric coding from JMP Genomics versions prior to 5.1 Value Ordering for Nominal Color Variable Value to Use to Replace Highest Values Value to Use to Replace Lowest Values Variable Containing Names of Marker Variables Variable Gene Selection Method Variables By Which to Merge Exon Annotation Data Variables By Which to Merge Tx Annotation Data Variables Defining Blocks Variables Defining Groups Variables Defining Plotting Groups Variables Defining the One-Way Classification Variables for QC Plotting Groups Variables to Keep in Linkage Map Data Set Variables to Keep in Output Variables to Keep in Output or By Which to Merge Annotation Data Variables to Retain in Linkage Map Data Set Variables Whose Rows are to be Clustered Variance Component Effects Variant Weights Where Clause for Subsetting Input Data Set in Test Run Width of Positional Group Workflow Folder Workflow Output Name Workflow to Journal Workflow to Run