BiocCheck Summary | Using BiocCheck | When should BiocCheck be run | Installing BiocCheck | Interpreting BiocCheck output | Installation | Deprecated Package Checks | Remotes Usage Check | LazyData Usage Check | Version Checks | Package and File Size Check | biocViews Checks | Build System Compatibility Checks | DESCRIPTION checks | NAMESPACE checks | .Rbuildignore checks | BiocCheck output folder check | Check for inst/doc folder | Vignette Checks | Checking Install or Update Package Calls in R code | Coding Practices Checks | Function length checking | man page checking | NEWS checks | Unit Test Checks | Formatting checks | Duplication checks | bioc-devel Subscription Check | Support Site Registration Check | BiocCheckGitClone | Using BiocCheckGitClone | Installing BiocCheckGitClone | Interpreting BiocCheckGitClone output | Bad File Check | CITATION checks | Expanding BiocCheck | SessionInfo

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()

AnVILPublish | Package installation | Package load | Requirements | Best practices | The gcloud SDK and GCPtools | Quarto software | Creating or updating workspaces | From package source | From collections of Rmd files | Updating notebooks or workspace permissions | Updating workspace notebooks from vignettes | Adding user access credentials to share the notebook | Vignette and .Rmd best practices | Orientation | Additional notes on .Rmd conversion | Session info

Installation | File Management | List Azure Blob Storage Container Files | Uploading a file | Deleting a file | Downloading from the ABS | Folder-wise upload to ABS | Folder-wise download from ABS | The DATA tab | mtcars example | Uploading data | Downloading data | Delete a row in the table | Delete entire table | Bug Reports | Session information

Installation | Additional Setup | Use in the AnVIL cloud | Local use | Graphical interfaces | Working with Google cloud-based resources | Using gcloud_*() for account management | Using gsutil_*() for file and bucket management | Using av*() to work with AnVIL tables and data | Tables, reference data, and persistent files | Using avtable*() for accessing tables | Using avdata() for accessing Workspace Data | Using avstorage() and workspace files | Using avnotebooks*() for notebook management | Using avworkflows_*() for workflows | Using avworkspace_*() for workspaces | Session Info

Overview | Setting up a package to use a Hub | New Hub package | Notify Bioconductor team member | Building the package | inst/extdata/ | inst/scripts/ | vignettes/ | R/ | man/ | DESCRIPTION / NAMESPACE | Data objects | Confirm Valid Metadata | Package review | Additional resources to existing Hub package | Converting a non AnnotationHub annotation package or non ExperimentHub | Bug fixes | Update the resource | Update the metadata | Remove resources | Versioning | Visibility | Storage of Data Files | Hosting Data on a Publicly Accessible Site | Uploading Data to Microsoft Azure Genomic Data Lake | R Interface with R package | Command Line via AWS S3 CLI | Utilizing the Bioconductor Docker container | Validating | Example metadata.csv file and more information

BiocBaseUtils | Installation | Load Package | Assertions | Logical | Character | Numeric | Slot replacement | show method | Contributing | Session Info

Installation | Quick start | Up to speed with AnVIL | Use in the AnVIL cloud | Local use | Graphical interfaces | For end users | Fast binary package installation | Working with Google cloud-based resources | Using gcloud_*() for account management | Using gsutil_*() for file and bucket management | Using av*() to work with AnVIL tables and data | Tables, reference data, and persistent files | Using avtable*() for accessing tables | Using avdata() for accessing Workspace Data | Using avbucket() and workspace files | Using avnotebooks*() for notebook management | Using avworkflows_*() for workflows | Using avworkspace_*() for workspaces | Using drs_*() for resolving DRS (Data Repository Service) URIs | For developers | Set-up | Service APIs | Construction | Invoke endpoints | Process responses | Test endpoints | Service implementations | Extending the Service class to implement your own RESTful interface | Support, bug reports, and source code availability | Appendix | Acknowledgments | Session info

BiocAzul | Installation | Package Loading | Introduction | Basic Usage | Connecting to the AnVIL Data Explorer | Listing Catalogs | Exploring Projects | Exploring Facets | Filtering and Queries | Integration with Terra | Conclusion | Session Information

Introduction | Creation and masking | Analytic utilities | Exporting to file | Session Information

Introduction | Installation | Import and Export | The BiocFile Class | CompressedFile | For developers | Converting existing "File" Classes | Creating classes and methods that extend BiocFile's class and methods | Session info

AnVILVRS | Introduction | Installation | Loading and Setup | Usage | Translating Variant Identifiers | Allele Object Retrieval | Variant Retrieval from Allele Object | Calculating Cohort Allele Frequency | Population Descriptor table download | SeqRepo reference data | Cohort Allele Frequency (CAF) calculation | Session Info

Introduction | Install and load the package | ZarrArray objects | Construction | Array and matrix operations | Other operations | Write an array-like object to disk in Zarr format | Session information

BiocPkgDash | Introduction | Comparison to Bioconductor Build Results | Installation | Loading | Dashboard display | Filtering packages | GitHub topic filter | Badges | Downloading the badge wall | Status | Dependencies | Metadata | Session Information

Introduction: Basic concepts of Dockstore and Bioconductor | Working with the Dockstore API in Bioconductor | Appendix | Acknowledgments | Session info

Installation | Workflow setup: DESeq2 | Setting up the workspace and choosing a workflow | Retrieving the configuration | Updating workflows | Changing the inputs / outputs | Update configuration locally | Set a workflow configuration for reuse in AnVIL | Running and stopping workflows | Running a workflow | Monitoring workflows | Stopping workflows | Managing workflow output | Workflow files | Workflow information | Session information

Introduction | Install and load the package | A quick overview of the functionality available in the package | Explode CIGAR strings | Tabulate CIGAR operations | Calculate the number of positions spanned by a CIGAR | Trim CIGAR strings along the reference or query space | Turn CIGAR strings into ranges of positions | Project positions from query to reference space and vice versa | Project sequences from one space to the other | Session information

Bioc.gff | Introduction | Installation | Loading packages | Usage | Reading GFF Files | Using the import function | Selectively importing ranges | Using the readGFF function | Reading remote GFF files | Conversion to GFF | GFF to TxDb | SessionInfo

What is S4? | The S4 class system | A different world | S4 in Bioconductor | S4 from an end-user point of view | Where do S4 objects come from? | How to manipulate S4 objects? | How to find the right man page? | Inspecting objects and discovering methods | Implementing an S4 class (in 4 slides) | Class definition and constructor | Getters | Extending an existing class | Slot inheritance | Method inheritance | Incremental validity method | What else?

Installation and Load | gcloud Command Line Utility | Check for gcloud SDK | gcloud Help | Access Token | Command Execution | List of available functions | gsutil Command Line Utility | Check for gsutil resources | gsutil Help | Disclaimer | SessionInfo

Introduction | Installation | Citing RaggedExperiment | RaggedExperiment class overview | Constructing a RaggedExperiment object | Using GRanges objects | Using a GRangesList instance | Using a list of GRanges | Using a List of GRanges with metadata | Accessors | Range data | Dimension names | colData | Subsetting | by dimension | by genomic ranges | *Assay functions | sparseAssay | Support for sparse matrix output | compactAssay | disjoinAssay | qreduceAssay | Coercion | from dgCMatrix to RaggedExperiment | Session Information | References

Introduction | Installation | Structure of ASCAT data | Converting ASCAT data to GRanges format | ASCAT to GRanges objects | ASCAT to GRangesList instance | Constructing a RaggedExperiment object from ASCAT output | Using GRanges objects | Using a GRangesList instance | Downstream Analysis | Session Information

Introduction | Install and load the package | The Seqinfo constructor | Seqinfo accessors | Operations on Seqinfo objects | Subset by seqnames | Rename, drop, add and/or reorder the sequences | Merge Seqinfo objects | Seqinfo objects as parts of higher-level objects | Session information

Introduction | Quick start | BatchtoolsParam interface | Defining templates | Use cases | Session info

Introduction | Error Handling | Messages and warnings | Catching errors | Identify failures with bpok() | Rerun failed tasks with BPREDO | Logging | Parameters | Setting a threshold | Log files | Worker timeout | Debugging | Accessing the traceback | Adding debug messages | Local debugging with SerialParam | Session info

Introduction | Basic use | Installing R | Installing BiocManager | Installing Bioconductor, CRAN, or GitHub packages | Previous releases | Version and validity of installations | Available packages | Updating old packages | Rationale | Pros of updating | Cons of updating | Balancing the Decision | Archived CRAN packages | Advanced use | Changing version | Unsupported R / Bioconductor versions | Managing multiple versions | Using the same R version | Offline use | Offline config.yaml | How it works | Troubleshooting | Package not available | Cannot load BiocManager | Timeout during package download | Multiple BiocVersion installations | Errors determining Bioconductor version | Session information

BiocHubsShiny | Installation | Loading the package | Display of resources | Filtering | Selection | Import | Session Info

Introduction | Install and load the required packages | The test datasets | Sparse vs dense representation | TENxMatrix vs HDF5Matrix objects | Bring the sparse dataset in R | Bring the dense dataset in R | Create the test datasets | Block-processed normalization and PCA | Code used for normalization and PCA | Block processing and block size | Monitoring memory usage | Normalization and PCA of the 27,998 x 12,500 test dataset | Normalization | TENxMatrix (sparse) | HDF5Matrix (dense) | HDF5Matrix as sparse | On-disk realization of the normalized datasets | PCA | Comprehensive timings obtained on various machines | Timings for DELL XPS 15 laptop | Timings for Supermicro SuperServer 1029GQ-TRT | Timings for Apple Silicon Mac Pro | Timings for Intel Mac Pro | Discussion | TENxMatrix (sparse) vs HDF5Matrix (dense) | Hybrid approach | A note about memory usage | Main takeaways | Session information

Introduction | Installation | The Array virtual class | The extract_array() generic function | Block processing of array-like objects | Other functionalities | Session information

Introduction | Install and load the package | The h5mread() function | Basic example | An example involving sparse data | A note about COO_SparseArray objects | Other functionality provided by the h5mread package | h5dim() and h5chunkdim() | Utility functions to manipulate the dimnames of an HDF5 dataset | H5File objects | Session information

Introduction | Install and load the package | The SparseArray virtual class and its two concrete subclasses | SVT_SparseArray objects | Construction | SVT_SparseArray vs COO_SparseArray | The SparseArray API | The core array API | type() and is_sparse() | is_nonzero() and the nz*() functions | Subsetting and subassignment | Summarization methods (whole array) | Operations from the Arith, Compare, Logic, Math, Math2, and Complex groups | The 2D API | SVT_SparseMatrix objects | Transposition | Combine multidimensional objects along a given dimension | matrixStats methods | rowsum() and colsum() | Matrix multiplication and cross-product | Other operations | Generate a random SVT_SparseArray object | Read/write a sparse matrix from/to a CSV file | Comparison with dgCMatrix objects | "SVT layout" vs "CSC layout" | Working with a big sparse dataset | Learn more | Session information

Introduction | Installation | Functions defined in the package | list_UCSC_genomes() | get_UCSC_chrom_sizes() | list_UCSC_tracks() | fetch_UCSC_track_data() | UCSC_dbselect() | Session information

UniProt.ws | Configuring UniProt.ws | Using UniProt.ws | sessionInfo()

Motivation | HTSlib version | Use | Find headers | Compile and link against the library | Implementation notes

Workspaces | Listing workspaces | Caveats | Current workspace | Setting the current workspace | Namespace and workspace | Cloning a workspace | Deleting a workspace | Notebooks | Localize / Delocalize | Workflows | Listing current workflow runs | Listing workflow inputs | sessionInfo

Introduction | Out-of-sync objects | The updateObject() generic function | A tedious process | updateBiocPackageRepoObjects() | List of tools provided by the updateObject package | Session information

Installation | Introduction | Overview | Cloud Platforms | Developer Note | Base generics | Table generics | Workspace generics | Workflow generics | Notebook generics | sessionInfo

Introduction | GRanges: Genomic Ranges | Splitting and combining GRanges objects | Subsetting GRanges objects | Basic interval operations for GRanges objects | Interval set operations for GRanges objects | GRangesList: Groups of Genomic Ranges | Basic GRangesList accessors | Combining GRangesList objects | Basic interval operations for GRangesList objects | Subsetting GRangesList objects | Looping over GRangesList objects | Interval overlaps involving GRanges and GRangesList objects | Finding the nearest genomic position in GRanges objects | Session Information

Introduction | Installation | Background | GDSArray | DelayedDataFrame | VariantExperiment class | slot accessors | Coercion methods | From VCF to VariantExperiment | From GDS to VariantExperiment | customization for certain gds types | Subsetting methods | two-dimensional subsetting | $ subsetting | Range-based operations | Save / load VariantExperiment object | save VariantExperiment object | load VariantExperiment object | Session Info

Introduction | Package installation | GDS format introduction | Genomic Data Structure (GDS) | GDSArray, GDSMatrix, and GDSFile | GDSArray, GDSMatrix, and DelayedArray | GDSFile | GDSArray methods | slot accessors. | Available GDS nodes | dim(), dimnames() | [ subsetting | some numeric calculation | Internals: GDSArraySeed | sessionInfo

How could I generate a manifest file with filtering of Race and Ethnicity? | How can I get the number of cases with RNA-Seq data added by date to TCGA project with GenomicDataCommons?

Introduction | Implementing the seed class | Class definition | Constructor | The seed contract | dim() and dimnames() | extract_array() | What to import? | Testing | Implementing high-level classes ADSArray and ADSMatrix | ADSArray class definition | The ADSArray() constructor | ADSMatrix class definition | Going from ADSArray to ADSMatrix | Going from ADSMatrix to ADSArray | Implementing optimized backend-specific methods | What to export?

What is the GDC? | Quickstart | Installation | Check connectivity and status | Find data | Download data | Metadata queries | Clinical data | General metadata queries | Basic design | Usage | Querying metadata | Creating a query | Retrieving results | Fields and Values | Facets and aggregation | Filtering | Authentication | Datafile access and download | Data downloads via the GDC API | Bulk downloads | BAM slicing | Use Cases | Cases | How many cases are there per project_id? | How many cases are included in all TARGET projects? | How many cases are included in all TCGA projects? | What is the breakdown of sample types in TCGA-BRCA? | Fetch all samples in TCGA-BRCA that use "Solid Tissue" as a normal. | Get all TCGA case ids that are female | Get all TCGA-COAD case ids that are NOT female | Get all TCGA cases that are missing gender | Get all TCGA cases that are NOT missing gender | Files | How many of each type of file are available? | Find gene-level RNA-seq quantification files for GBM | Slicing | Get all BAM file ids from TCGA-GBM | Troubleshooting | SSL connection errors | sessionInfo() | Developer notes

Background | Workflow | Genes and gene details | ssms | convert to VRanges | OncoPrint

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 | Installation | Basic usage | Using forgeBSgenomeDataPkgFromNCBI() | Using forgeBSgenomeDataPkgFromUCSC() | Final steps | sessionInfo()

Introduction | Vector-like and list-like objects | Vector-like objects | Subsetting a vector-like object | Concatenating vector-like objects | Looping over subsequences of vector-like objects | List-like objects | Vector Annotations | Session Information

Introduction | Installing the txdbmaker package | Using makeTxDbFromUCSC | Using makeTxDbFromBiomart | Using makeTxDbFromEnsembl | Using makeTxDbFromGFF | Saving and Loading a TxDb Object | Using makeTxDbPackageFromUCSC and makeTxDbPackageFromBiomart | Session Information

Introduction | Load the aligned reads and their sequences from a BAM file | Compute the original query sequences | Mismatches, indels, and gaps | Put the read sequences and reference sequences "side by side" | OLD STUFF (needs to be recycled/updated) | Load paired-end reads from a BAM file | sessionInfo()

Introduction | Installing the GenomicFeatures package | Obtaining a TxDb object | Retrieving Data from a TxDb object | Pre-filtering data based on Chromosomes | Retrieving data using the select() method | Methods for returning GRanges objects | Working with Grouped Features | Predefined grouping functions | Getting the actual sequence data | Session Information

Overview | Using probe packages | Basic functions | Reverse and complementary sequence | Matching sets of probes against each other | Base content | Relating to the features of an AffyBatch | Some sequence related "preprocessing and quality" plots

Introduction | Anatomy of a SummarizedExperiment | Assays | 'Row' (regions-of-interest) data | 'Column' (sample) data | Experiment-wide metadata | Constructing a SummarizedExperiment | Top-level dimnames vs assay-level dimnames | Common operations on SummarizedExperiment | Subsetting | Getters and setters | Range-based operations | Interactive visualization | Session information

Introduction | Quick start | The BiocParallel Interface | Classes | BiocParallelParam | register()ing BiocParallelParam instances | Functions | Parallel looping, vectorized and aggregate operations | Parallel evaluation environment | Error handling and logging | Locks and counters | Use cases | Single machine | Forked processes with MulticoreParam | Clusters of independent processes with SnowParam | Ad hoc cluster of multiple machines | Ad hoc Sockets | MPI | Clusters with schedulers | Cluster-centric | R-centric | Analyzing genomic data in Bioconductor | For developers | For server administrators | sessionInfo

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

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 | 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()

Background | Support for existing organisms | File format for new organism | Example File | Contacting us with your new file

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

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

Scope | Essentials | Use of bplapply() and RNGseed= | Use with bpiterate() | Use with bptry() | Relationship between RNGseed= and set.seed() | bpstart() and random number streams | Relationship between bplapply() and lapply() | Implementation notes | sessionInfo()

Introduction | Installation | DelayedDataFrame class | class extension | slot accessors | lazyIndex slot | DelayedDataFrame methods | Coercion methods | Subsetting methods | subsetting by [ | subsetting by [[ | rbind/cbind | sessionInfo

Introduction | Installation | HubPub | Creating a Hub styled package | Adding a resource to the metadata file | Publishing the resource to AWS S3 | Session Information

Motivation | Deriving a simple class | Overview | Defining the class and its constructor | Defining a validity method | Defining a getter method | Some comments on package organization | Deriving a class with custom slots | Class definition | Defining the constructor | Creating getter methods | For 1D data structures | For 2D data structures | For SummarizedExperiment slots | Defining the validity method | Creating a show method | Creating setter methods | Other types of modifying functions | Enabling subsetting operations | Getting a subset | Assigning a subset | Defining combining methods | By row | By column | Defining coercion methods | Coercion from SummarizedExperiment | Deriving from a RangedSummarizedExperiment | Unit testing procedures | Constructor | Getters | Setters | Other modifying functions | Subsetting methods | Combining methods | Documentation | Session information

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