Introduction | Setting up the data | Launching the interface | Description of the user interface | Header | Body | Overview of panel types | Reduced dimension plots | Column data plots | Feature assay plots | Row data plots | Sample assay plots | Row data tables | Column data tables | Heat maps | Description of iSEE functionality | Coloring plots by sample attributes | Controlling point aesthetics | Faceting | Zooming in and out | FAQ | Additional information | Session Info | References

Introduction | Multiple selections | Basic use | Selection effects | Saving selections | Single selections | Dynamic selections | Session Info

Changing the default start configuration | Data parameters | Overview | Setting the Y-axis | Setting the X-axis | Configuring the type of dimensionality reduction | Configuring the type of assay data | Visual parameters | Configuring default visual parameters | Linking point aesthetics to variables | Configuring plot facets | Selection parameters | Writing your own tour | Further reading | Session Info | References

Background | Defining colormaps | Colormaps for continuous variables | Colormaps for categorical variables | The colormap hierarchy | Specific and shared colormaps | Searching for colors | Creating the ExperimentColorMap | Benefits | Demonstration | Session Info | References

Background | Defining custom functions | Minimum requirements | Example of custom plot panel | Example of custom table panel | Handling active and saved selections | Advanced extensions | Session Info | References

Overview | Using out-of-memory matrices | Downsampling points | Changing the interface | Comments on deployment | Session Info

iSEEindex resources | Overview | Implementation | Built-in resources | iSEEindexHttpsResource | Structure | Caching | iSEEindexLocalhostResource | iSEEindexRcallResource | iSEEindexS3Resource | iSEEindexRunrResource | Reproducibility | Bibliography

Overview | Example | Further reading | Where can I find a comprehensive introduction to r Biocpkg("iSEE")? | Session information | References

Motivation | Background | Features | Demonstration data | CollapsedVCF and ExpandedVCF | Fields available for the definition of filter rules | Usage of VCF filter rules | Filter rules using a single field | Filter rules using multiple fields | Calculations in filter rules | Functions in filter rules | Pattern matching in filter rules | Using ALT data in the fixed slot of VCF objects | ExpandedVCF objects | CollapsedVCF objects | Combination of multiple types of VCF filter rules | Session info | References

Overview | Downsampling for demonstration | Basic workflow | Advanced options | Session information | References

Feature | Implementation | Supported web browsers | Usage | Vocal commands available | Session Info | References

Overview | Differential expression plots | Dynamically recalculated panels | Feature set table | App modes | Miscellaneous panels | Contributing to r Biocpkg("iSEEu") | Using example data sets | Documenting, testing, coding style and conventions | Looking for constants within r Biocpkg("iSEE") | What if I need a custom panel type? | Where can I find a comprehensive introduction to r Biocpkg("iSEE")? | Session information | References

Basics | Install iSEEpathways | Required knowledge | Asking for help | Citing iSEEpathways | Quick start to using to iSEEpathways | Reproducibility | Bibliography

Scenario | Demonstration | Example data | Experimental metadata | Feature identifiers | Gene expression | Differential expression analysis | Pathways | Mapping pathways to genes | Gene set enrichment analysis | Displaying additional pathway information | Live app | Trading off memory usage for speed | Reproducibility | Bibliography

Scenario | Demonstration | Example data | Pathway information | Live app | Reproducibility | Bibliography

Custom header and footer | Overview | Implementation | Example | Reproducibility | Bibliography

Basics | Install iSEEindex | Required knowledge | Asking for help | Citing iSEEindex | Quick start to using iSEEindex | Reproducibility | Bibliography

Example data | Differential expression | Set a default rounding configuration | Configuring rounding in individual panels | Reproducibility | Bibliography

Implementation | User-facing storage and access | Additional considerations | Example data | Supported methods | Limma | DESeq2 | edgeR | Live app | Comparing two contrasts | Reproducibility | Bibliography

Example data | Annotating data | Differential expression | Live app | Reproducibility | Bibliography

Basics | Install iSEEde | Required knowledge | Asking for help | Citing iSEEde | Quick start to using to iSEEde | Reproducibility | Bibliography

Introduction | Basics | Install iSEEhub | Required knowledge | Asking for help | Citing iSEEhub | Quick start to using to iSEEhub | The ExperimentHub pane | The Selected Dataset pane | Overview | The Info tab | The Config tab | The main iSEE app | Managing dataset dependencies | From the R console | From the live app | Reproducibility | Bibliography

Initial app configurations | Overview | Requirements | Example | Process for contributing | Reproducibility | Bibliography

Preliminary notes | Pre-requisites | Launching the Shiny Variant Explorer | Overall layout of the web-application | Input panel | Phenotypes | Genomic ranges | BED file | UCSC format | Ensembl-based annotation packages | Variants | Single-VCF mode | Multi-VCF mode | VCF scan parameters | Annotations | Frequencies panel | Overall frequencies | Phenotype-level frequencies | Filters panel | Views panel | Plots panel | Settings panel | Advanced settings | Genotypes | INFO key suffixes | Miscellaneous settings | Parallel settings | Session information | Global configuration | Vignette session | References

1 Introduction | 2 Before you start | 3 Quick start | 4 Additional controls and advanced functions | 5 Statistics | 6 Integration with other packages | 7 Notes

Introduction | Installation | Recurrent settings: TVTBparam | Data import | Genetic variants | List of genomic ranges | Phenotypes | Example | Adding allele frequencies | Adding overall frequencies | Adding frequencies within phenotype level(s) | Filtering variants | Definition of VCF filter rules | Control of VCF filter rules | Evaluation of VCF filter rules | Visualising data | Visualise INFO data by phenotype level on a genomic axis | Pairwise comparison of INFO data between phenotype levels | A taste of future... | Summarising Ensembl VEP predictions | Acknowledgement | Session info | References