KEGGREST | Installation | Overview | Exploring KEGG Resources with keggList() | Get specific entries with keggGet() | Search by keywords with keggFind() | Convert identifiers with keggConv() | Link across databases with keggLink()

ExperimentHub objects | Interactive retrieval of resources with BiocHubsShiny | Using ExperimentHub to retrieve data | Configuring ExperimentHub objects | Creating an ExperimentHub Package or Converting to an ExperimentHub Package | Troubleshooting | Accessing Behind A Proxy | Other configuration options for resource downloading | Group Hub/Cache Access | Default Caching Location Update | Option 1: Move cache and files to new location | Option 2: Create a system environment variable | Option 3: Delete the old cache | Session info

Accessing Genome-Scale Data | Non-model organism gene annotations | Roadmap Epigenomics Project | Ensembl GTF and FASTA files for TxDb gene models and sequence queries | liftOver to map between genome builds | sessionInfo

Version Info | Setup: The NHGRI GWAS catalog as an hg38-based GRanges | Resource: The chain file for hg38 to hg19 transformation | Action: liftOver

AnnotationHub objects | Interactive retrieval of resources with BiocHubsShiny | Using AnnotationHub to retrieve data | Configuring AnnotationHub objects | AnnotationHub objects in a cluster environment | Creating an AnnotationHub Package or Converting to an AnnotationHub Package | Troubleshooting | Accessing Behind A Proxy | Other configuration options for resource downloading | Session info

Overview | Troubleshooting | Accessing Behind A Proxy | Other configuration options for resource downloading | Invalid Cache | Corrupt Cache | sqlite file | redownload of sqlite file | index file | resource path | resource id | Corrupt Database | Cannot retrieve resource | Offline localHub usage | Group Hub/Cache Access | Lock file Troubleshooting | Permissions | Cannot lock file / no lock available | Default Caching Location Update | Option 1: Move cache and files to new location | Option 2: Create a system environment variable | Option 3: Delete the old cache

Sample data | Functionality | Common workflows | Quality assessment | Filtering and trimming | Using ShortRead for data exploration | Data I/O | readXStringColumns | Sorting | Summarizing read occurrence | Finding near matches to short sequences | Legacy support for early file formats | Session Info

Introduction | clusterGraph | distGraph

Introduction | Getting Started | Some Algebraic Manipulations | Random Graphs | Some Graph Algorithms | Special Types of Graphs | Coercion | Classes | References

Introduction | Acquire annotation on variants from a VCF file | Transforming the API response to GRanges | Further work | References

Overview | Contents | Usage | Package installation | Documentations | Accessing annotation data within a library | Accessing annotation data across libraries | Session Information

Overview | The chromLocation class | Summary

Introduction | Getting edge attributes | Setting edge attributes | Node Attributes | Default node attributes | Getting and setting node attributes

Introduction | Variant Call Format (VCF) files | Data import and exploration | Header information | Genomic positions | Genotype data | Info data | Import data subsets | Select genomic coordinates | Select VCF fields | Locating variants in and around genes | Amino acid coding changes | SIFT and PolyPhen Databases | Other operations | Create a SnpMatrix | Write out VCF files | Performance | References | Session Information

Introduction | The Data: Paired Tumor/Normal Breast Cancer Variants | Filter by Genomic Region | Introducing the filterVcf Method | Prefilters | Filters | FilterRules | Create the Filtered file | Look for SNPs in Regulatory Regions | Load CTCF Transcription Factor Binding Regions Identified in MCF-7 Breast Cancer Cell Line | Find SNPs in CTCF Binding Regions | Conclusion | Appendix: Filter by Genomic Region | Bibliography

Basic notations/Preliminaries | Basics Notations | Examples in use | Working with the Bioconductor graph class | Algorithms from BGL | Depth First Search | Breadth First Search | Shortest paths | Minimum spanning tree | Connected components | Maximum Flow | Sparse Matrix Ordering | Edge connectivity and minimum disconnecting set | Topological sort | Isomorphism | Vertex Coloring | Wavefront, Profiles | Betweenness Centrality and Clustering | Algorithms built on RBGL | Min-Cut | highlyConnSG | Algorithms independent from RBGL | maxClique | is.triangulated | separates | kCores | kCliques

Getting started with OrganismDbi | Making your own OrganismDbi packages

Prerequisites | Getting started | Use with R markdown v1 | Document header | Author affiliations | Abstract and running headers | Style macros | Code chunks | Figures | Simple figures | Figure captions | Alternative figure sizes | Accessibility considerations | Tables | Equations | Cross-references | Margin notes | Bibliography | References | Session info

Example data | Extending reads | Coverage, islands, and depth | Processing multiple lanes | Peaks | Differential peaks | Placing peaks in genomic context | Visualizing peaks in genomic context | Version information

Introduction | Input | RfunctionscanBam and ScanBamParam | Using BAM index files | Other ways to work with BAM files | Large bam files | Views | Assembling a BamViews instance | Using BamViews instances | Directions | (APPENDIX) Appendix | Genomic ranges of interest | BAM files

Introduction | Selecting genes that appear useful for prediction | Session Information

Introduction | Quick Start | Overview of classes and functions | GenomicFiles class | Functions | Queries across files: reduceByRange and reduceRanges | Pileup summaries | Basepair-level $t$-test with case / control groups | Queries within files: reduceByFile and reduceFiles | Counting read junctions | Coverage 1: reduceByFile | Coverage 2: reduceFiles | Coverage 3: reduceFiles with chunking | Chunking | Ranges in a file | Records in a file | sessionInfo()

Introduction | Parameter Settings | Session Information

GeneSet | GeneColorSet | GeneSetCollection

graphBAM class | Introduction | A simple graph represented using graphBAM class | Mice gene interaction data for brain tissue (SAGE data) | MultiGraphs | A simple MultiGraph example | MultiGraph representation of mice gene interaction data. (SAGE)

Introduction | Comparing old and new | A quick tour | The eSet object: high-throughput experiments | assayData: high-throughput data | phenoData: sample covariates | featureData: feature covariates | experimentData: experiment description | annotation: assay description | Important eSet methods | Additional eSet methods | Subclasses of eSet | ExpressionSet | MultiSet and SnpSet | Comments on assayData: high-throughput data storage | Extending eSet | Implementing a new class: a SwirlSet example | Versioned | Versioned versus VersionedBiobase | Adding Versioned information to your own classes | Summary | Session Information

A note on esApply | Session Information

Introduction | The graph class | Methods of graphs | Some Details | Representation of Edges | Multi-graphs | Methods | Use Cases | Bipartite Graphs

Overview | Establishing a vocabulary of terms | Use Case: adding a term to the vocabulary | Use Case: updating BioConductor website | Querying a repository | Generating HTML

Overview | CRAN-style Layout | Extracting vignettes | Generating the control files | Generating the HTML | Design and extension notes | Details on HTML generation | A note on the htmlValue method for PackageDetail

Overview | Creating an AnnotationHub Package or Converting to an AnnotationHub Package | Historical vignettes

Overview | Creating an ExperimentHub Package or Converting to an ExperimentHub Package | ExperimentHub_docker

Version Info | Background | Set Up | Exploring variants in the TRPV gene family | Examine header data in a vcf file | Convert gene symbols to gene ids | Create gene ranges | Extract variant subsets | Variant location in the gene model | Amino acid coding changes in non-synonymous variants | Exploring Package Content | sessionInfo()

1 AnnotationDb objects and the select method | 2 ChipDb objects and the select method | 3 OrgDb objects and the select method | 4 Using select with GO.db | 5 Using select with TxDb packages | 6 Using select with EnsDb packages

1 Introduction | 2 Data preparation | 3 Filtering volcano plot | 4 Rejection count plots

Chromosome bands | Data Preparation | Methods | Utility functions | Hypergeometric Testing | GSEA using linear models

Abstract | Sequencing Resources | Ranges Infrastructure | DNA /amino acid sequence from FASTA files | Reads from FASTQ files | Aligned Reads from BAM files | Called Variants from VCF files | Genome Annotations from BED, WIG, GTF etc files

Version Info | Introduction | Installation and Use | Biological Background | Sequence Search | Minimal Example | Sample Workflow: an extended example | Biological Summary | Exploring Package Content

Version Info | Sample Workflow | Installation and Use | Exploring Package Content | Pre-Processing Resources | Affymetrix 3'-biased Array | Affymetrix Exon ST Arrays | Affymetrix Gene ST Arrays | Affymetrix SNP Arrays | Affymetrix Tiling Arrays | Nimblegen Arrays | Illumina Expression Microarrays

Introduction | Preliminaries | Building an ExpressionSet From .CEL and other files | Building an ExpressionSet From Scratch | ExpressionSet Basics | What was used to create this document

Introduction | Filter classes | Usage | Using AnnotationFilter in other packages | Session information

Overview | Using the Browser | Accessing PubMed information | Generating HTML output for your abstracts | Session Information

1 Authoring package vignettes | 2 Structuring the document | A Session info | B Attached LaTeX packages | C Known issues

Initial work flow | Loading the data | Exploring the data | Saving computations | Improving computational performance | Parallel computation | Working with Rle-compressed HDF5 data | Session information

DE analysis with Raw TCGA data using Bioconductor's ExperimentHub and DESeq2 | Case Study | sessionInfo()

Introduction

Data | Distance Measures | Session Information

Fitting Models to data

Overview | Whole Genome Plots | Single Chromosome Plots

Overview | Developers Tips | Session Information

Overview | Alternate methods | Data Analysis | Getting Started | Annotation Data | Build the Table | Session Information

Session Information