Creating a database connection | Setting up the data model | Fully fletched table editor

Option 1 | Option 2

Introduction | Installation | Load the package into R session | Load data | Top table | Model | Visualizations | Volcano plot | Highlight top genes or genes of interest | Additional fdr threshold | Interactive plot | Log-ratio plot | Color feature labels | Facet by variable(s) | Mixed input | Sort features | Based on significance | Display text | Significance star | Log fold change | Heatmap | Nested coefficient labels | Upset plot | Down-regulated genes | Return overlapping sets | Scatter plot | Highlight genes of interest and top genes | Interactive plot with feature annotation | Add correlation | Waterfall plot | Multiple coefficients | MA plot | Label top genes and genes of interest | Significant genes barplot | Session information

Detailed framework of the creation of the in-text table | Computation of the summary statistics | Export table to the requested format | Combine summary statistics table | Via the combine function | Manually | Statistics in rows | Statistics in rows, in an extra column | Statistics in an extra column | Data pre-processing | Appendix | Session information

Available options | Options for reporting | Colors | Dimension of the page | Options for visualization | Set back default palettes | Set up specific palettes | Page dimensions in report/presentation | Appendix | Session information

Variable(s) to summarize | Categorical variable | Counts of the entire dataset | Counts of categories | Sort categories | Inclusion of categories not available in the data | Count table for 'flag'-variables | Inclusion of total across categories | Continuous variable | Continuous and categorical variables in the table | Statistics of interest | Standard statistic set | Categorical table | Custom statistics formatting (Advanced) | Statistics by variable/group | Extra statistics | Rounding strategy | Number of decimals | Default number of decimals | Continuous variable | Custom stats function (Advanced) | Statistics layout | Table layout | Row and column variables | Row variable | Variable in separated column | Row ordering | Common order for all row variables | Different orders for each row variable | Row order based on the total of a column category | Row order based on a custom specified function | Row variable labels | Based on dataset | Custom | Inclusion of row/column categories not available in the data | Default | Summary variable in columns | Inclusion of summary variables in case one variable is specified | Inclusion of the counts per group in case of missing values | Total | Summary | Total for the column header | Current datasset | External dataset | Remove total in column header | Percentage | Dataset | Variables to compute percentage by | Percentage of the number of records | Total across columns | Inclusion | Label | Total across rows | Inclusion as separated category | Labels | Title and footnote | Appendix | Session information

Introduction | Data format | Subject information | Subject disposition | Demographics | Baseline disease characteristics | Medical History and Concomitant Diseases | Efficacy Analyses | Safety Analyses | Adverse Events | Treatment-emergent summary table | Treatment-emergent incidence table | Events occuring in at least one subject | Events occuring in at least 25% of all subjects | Treatment-emergent worst-case table | Laboratory safety | Table of laboratory abnormalities | Electrocardiogram | Vital signs | Treatment-emergent vital signs abnormalities | Pharmacokinetics analysis | Appendix | Session information

Load packages and data | Output formats | Static table for Word/Powerpoint | General format | Style: report or presentation | Interactive table for html | Data frames for R | Final table | Full table in long format | Differences between the format | Custom aesthetics | Colors | Dimension of the page | Further info on asthetics | Set back default palettes | Export table to a separated file | Export table of pre-computed summary statistics | Text formatting | Superscript/subscript | Bold and greek letters | Create multiple tables by a variable | Listing | Filter records in a table | Appendix | Session information

Introduction | Data format | Create your tables | Table formatting/export | Advanced users | Visualization | Aesthetics | Appendix | Session information

Load packages and data | Compute summary statistics | Visualization for A4 document | Visualization for presentation | Palettes | Custom palettes via arguments in the function | Color palette | Shape and linetype palettes | Custom palettes via setting global options | Coloring palettes | Set back default palettes | Visualization without count table | Visualization by facets | Customize your visualization | Appendix | Session information

Basics of handling a database in R | A simple table editor | Advanced table editor (flat, joined table). | Advanced table editor (partial table). | Above and beyond

Hide rows completely | Read-only access

Patient profiles | Data visualization | Visualization of individual profiles | Explore the visualization data | Link with patient profiles | Spaghetti plot of time profile | Scatterplot | eDish plot | Visualization of time-intervals | Visualization of summary statistics | Categorical variables | Compute count statistics | Sunburst | Treemap | Barplot | Continuous variable | Compute summary statistics | Plot error bars/confidence intervals | Boxplot | Multiple visualizations in a loop | Watermark | Palettes | Set palette for the entire session | Appendix | Session info

Process and clean the data | Data transformation | Analysis | Fitting marginal (on-axis) data | Optimization algorithms | Custom marginal fit | Compute expected response for off-axis data | (Generalized) Loewe model | Highest Single Agent | Bliss Independence | Alternative Loewe Generalization | Plot 2D cross section of response surface | Statistical testing | meanR | maxR | Effect sizes and confidence interval | Analysis in case of variance heterogeneity | Analysis of multiple experiments

Create an example report | File structure | Input | Output | Template reports | Render a clinical data review report | Production | Create a report for production | Create redirect page | Convert to .aspx format | Zip and send the report to collaborators | Add metadata | Development | Modular framework | (Re-)run part(s) of the report | Create the final clinical data report from the Markdown reports | Debug a sub-report | Optimization for big clinical trial data | Optimize the report creation | Optimize the report loading time | Optimize the report structure | Appendix | Session info

Data format | Annotate data | Filter data | Transform data | Process data | Appendix | Session info

Introduction | Input data | Data format | Example SDTM dataset | Example ADaM dataset | Creation of the plot modules | General | Text module | Wide format | Long format | Table format (listing) | Customization for multiple variables | With grouping | Interval/Range module | Adverse events | Exposure | Concomitant medications | Missing starting/end time | Default imputation | Imputation based on an external dataset | Custom specification for missing and partial dates | Specification of time limits | Non-alignment across subjects | Event module | Color/symbol | Line module | Color/symbols of each observation | Reference range | Display reference range indicators | Range of the y-axis based on the observations or the reference range | Subset of interest | Subset based on extra variable | Set of subjects of interest | Specify colors/shapes | Missing values | Order of the categories | Palettes | Set palette for the entire session | Palette for standard CDISC variables | Time transformation | Creation of subject report | Example report | SDTM dataset | ADaM dataset | Reference lines | Specify custom reference lines | Reference lines from subject visits | Bookmarks | Time alignment | Visualizations aligned across domains and subjects | Visualizations aligned across subjects only for a specific domain | Visualizations not aligned across domains | Visualizations aligned per subject | Optimization of patient profiles creation | Appendix | Session information

Introduction | Dataset | Creation of patient profiles | Demographics | Medical history | Concomitant medications | Treatment exposure | Adverse events | Laboratory measurements | Vital signs | Electrocardiogram | Creation of the reports | Session information

Introduction | Data pre-processing | Data import | Example datasets | ADaM | SDTM | Variable labels | Get parameter label from its parameter code | Visualizations | Palette for CDISC variables | Normal reference range indicators | Get default palettes | Tables | Rounding | Display data in an interactive table | Comparison of tables | Reporting | Include list of objects in a Rmarkdown document | Static visualizations (ggplot2) | Interactive visualizations (plotly) | htmltools::tagList | Inclusion in a separated chunk | Tables (flextable) | Appendix | Session info

Marginal monotherapy curves | Null models of no synergy | Occupancy | Classical Loewe model | Generalized Loewe model | Highest Single Agent | Bliss independence model | Alternative Loewe Generalization | Calculation procedure | Synergy evaluation assuming equal variances for on- and off-axis points | meanR | maxR | Synergy evaluation in case of variance heterogeneity | Adapted meanR | Adapted maxR | Bootstrapping under unequal variances | Advantages of unequal and model methods compared to assumption of equal variances | Effect size for off-axis points | Confidence interval\label | Standard error\label | Single effect measure | Confidence interval | On resampling residuals\label