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

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

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

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 | 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

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

Introduction | Build reports | Personal build report | Download statistics | Package details | Package Explorer | Dependency graphs | Working with dependency graphs | Graph visualization | Integration with r Biocpkg("BiocViews") | Dependency burden | Identities of maintainers | Provenance

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

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

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 | 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

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

Version-bump-and-branch-creation-HOWTO | A. Introduction | B. Preliminary steps | C. Version bumps and branch creation for software packages | C1. Comment out all builds in crontab on central BioC 3.23 builder | C2. Ask people to stop committing/pushing changes to the BioC git server | C3. Modify packages.conf to block all commits | C4. Disable hooks | C5. Log on the machine where you've performed the preliminary steps | C6. Checkout/update the RELEASE_3_23 branch of the manifest repo | C7. Set the BBS_HOME, WORKING_DIR and MANIFEST_FILE environment variables | C8. Run bump_version_and_create_branch.py | C9. Check bump_version_and_create_branch.log | D. Version bumps and branch creation for data-experiment packages, workflows, and books | D1. Data-experiment packages | D2. Workflows | D3. Books | E. Branch creation for data-annotation packages | F. Finishing up | F1. Enable push access to new RELEASE_3_23 branch | F2. Tell people that committing/pushing to the BioC git server can resume | F3. Switch BBS_BIOC_GIT_BRANCH from devel to RELEASE_3_23 on central BioC 3.23 builder | F4. Sync all core Bioconductor packages hosted on GitHub

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

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

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

Pre-release | R versions | Six weeks before | Four weeks before | Three weeks before | Two weeks before | One week before | Day before we branch (D-2): | Day we branch (D-1): | Release day | Post-release | Week after the Release (D+):

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

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

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 | Supported Formats | Tested 10X Products | Bioconductor implementations | Installation | Load the package | Description | Procedure | Dataset versioning | File classes | TENxFile | ExperimentHub resources | TENxH5 | import TENxH5 method | TENxMTX | import MTX method | TENxFileList | TENxPeaks | TENxFragments | Session Information

Introduction | Supported Formats | Tested 10X Products | Bioconductor implementations | Installation | Load the package | Description | Procedure | Dataset versioning | File classes | TENxFile | ExperimentHub resources | TENxH5 | import TENxH5 method | TENxMTX | import MTX method | TENxFileList | TENxPeaks | TENxFragments | Session Information

terraTCGAData | Installation | Overview | Data | Requirements | Loading packages | gcloud sdk installation | Default Data Workspace | Clinical data resources | Clinical data download | Assay data resources | Summary of sample types in the data | Intermediate function for obtaining only the data | MultiAssayExperiment | Session Info

terraTCGAData | Installation | Overview | Data | Requirements | Loading packages | gcloud sdk installation | Default Data Workspace | Clinical data resources | Clinical data download | Assay data resources | Summary of sample types in the data | Intermediate function for obtaining only the data | MultiAssayExperiment | Session Info

Branching Annotation | Set up nebbiolo1 | Create new annotation repo on devel master builder (nebbiolo1) | rsync annotations from current release | Remove symlinks for old R versions for windows and mac on new devel | Set up <master.bioconductor.org> | Log on master as webadmin | Remove symlink and create empty annotation folder | Create a new annotation folder | Back to nebbiolo1 to run the propagation scripts | Update bioconductor.org/config.yaml to build landing pages for 3.23

Summary of the MultiAssayExperiment API | API Overview | Constructors | Accessors | Subsetting | Management | Reshaping | Combining | Coercion | Export | Notes

Summary of the MultiAssayExperiment API | API Overview | Constructors | Accessors | Subsetting | Management | Reshaping | Combining | Coercion | Export | Notes

Introduction | TENxIO Supported Formats | VisiumIO Supported Formats | Installation | Loading package | TENxVisium | Example from SpatialExperiment | Creating a TENxVisium instance | Importing into SpatialExperiment | TENxVisiumList | Creating a TENxVisiumList | Visium HD folder structure | Import Visium HD into SpatialExperiment | In-package example | Session Info

Introduction | TENxIO Supported Formats | VisiumIO Supported Formats | Installation | Loading package | TENxVisium | Example from SpatialExperiment | Creating a TENxVisium instance | Importing into SpatialExperiment | TENxVisiumList | Creating a TENxVisiumList | Visium HD folder structure | Import Visium HD into SpatialExperiment | In-package example | Session Info

Installation | Citing MultiAssayExperiment | A Brief Description | Choosing the appropriate data structure | Overview of the MultiAssayExperiment class | Components of the MultiAssayExperiment | ExperimentList: experimental data | Class requirements within ExperimentList container | colData: primary data | colData slot requirements | Note on the flexibility of the DataFrame | sampleMap: relating colData to multiple assays | sampleMap structure | Instances where sampleMap isn't provided | metadata | Creating a MultiAssayExperiment object: a rich example | Create toy datasets demonstrating all supported data types | sampleMap creation | Experimental data as a list() | Creation of the MultiAssayExperiment class object | Helper function to create a MultiAssayExperiment object | Helper functions to create Bioconductor classes from raw data | Integrated subsetting across experiments | Subsetting by square bracket [ | Subsetting by character, integer, and logical | the "drop" argument | More on subsetting by columns | Subsetting assays | Subsetting rows (features) by IDs, integers, or logicals | Subsetting rows (features) by GenomicRanges | Subsetting is endomorphic | Double-bracket subsetting to select experiments | Helpers for data clean-up and management | complete.cases | replicated | intersectRows | intersectColumns | mergeReplicates | combine c | Extractor functions | getWithColData | longForm & wideFormat | assay / assays | The Cancer Genome Atlas and MultiAssayExperiment | Dimension names: rownames and colnames | Requirements for support of additional data classes | Application Programming Interface (API) | Methods for MultiAssayExperiment | sessionInfo() | References

Installation | Citing MultiAssayExperiment | A Brief Description | Choosing the appropriate data structure | Overview of the MultiAssayExperiment class | Components of the MultiAssayExperiment | ExperimentList: experimental data | Class requirements within ExperimentList container | colData: primary data | colData slot requirements | Note on the flexibility of the DataFrame | sampleMap: relating colData to multiple assays | sampleMap structure | Instances where sampleMap isn't provided | metadata | Creating a MultiAssayExperiment object: a rich example | Create toy datasets demonstrating all supported data types | sampleMap creation | Experimental data as a list() | Creation of the MultiAssayExperiment class object | Helper function to create a MultiAssayExperiment object | Helper functions to create Bioconductor classes from raw data | Integrated subsetting across experiments | Subsetting by square bracket [ | Subsetting by character, integer, and logical | the "drop" argument | More on subsetting by columns | Subsetting assays | Subsetting rows (features) by IDs, integers, or logicals | Subsetting rows (features) by GenomicRanges | Subsetting is endomorphic | Double-bracket subsetting to select experiments | Helpers for data clean-up and management | complete.cases | replicated | intersectRows | intersectColumns | mergeReplicates | combine c | Extractor functions | getWithColData | longForm & wideFormat | assay / assays | The Cancer Genome Atlas and MultiAssayExperiment | Dimension names: rownames and colnames | Requirements for support of additional data classes | Application Programming Interface (API) | Methods for MultiAssayExperiment | sessionInfo() | References

Introduction | Installation | Load the package | Last release version | Archived installations | Docker installation | Bioconductor installations | P3M installations | CRAN installations from the source archive | Repository URLs | Package validity | Session Information

Integrating an HDF5 backend for MultiAssayExperiment | Dependencies | HDF5Array and DelayedArray Constructor | Writing to a file with dimnames | Importing HDF5 files | Using a DelayedMatrix with MultiAssayExperiment | SummarizedExperiment with DelayedMatrix backend | Session info

Component slots | colData - information on biological units | ExperimentList - experiment data | sampleMap - relationship graph | metadata | Subsetting | Single bracket [ | Subsetting by genomic ranges | Double bracket [[ | Patients with complete data | Row names that are common across assays | Extraction | assay and assays | Summary of slots and accessors | Transformation / reshaping | longForm | wideFormat | MultiAssayExperiment class construction and concatenation | MultiAssayExperiment constructor function | prepMultiAssay - Constructor function helper | c - concatenate to MultiAssayExperiment | Examples | UpsetR "Venn" diagram | Kaplan-meier plot stratified by a clinical variable | Multivariate Cox regression including RNA-seq, copy number, and pathology | Session info

Integrating an HDF5 backend for MultiAssayExperiment | Dependencies | HDF5Array and DelayedArray Constructor | Writing to a file with dimnames | Importing HDF5 files | Using a DelayedMatrix with MultiAssayExperiment | SummarizedExperiment with DelayedMatrix backend | Session info

Component slots | colData - information on biological units | ExperimentList - experiment data | sampleMap - relationship graph | metadata | Subsetting | Single bracket [ | Subsetting by genomic ranges | Double bracket [[ | Patients with complete data | Row names that are common across assays | Extraction | assay and assays | Summary of slots and accessors | Transformation / reshaping | longForm | wideFormat | MultiAssayExperiment class construction and concatenation | MultiAssayExperiment constructor function | prepMultiAssay - Constructor function helper | c - concatenate to MultiAssayExperiment | Examples | UpsetR "Venn" diagram | Kaplan-meier plot stratified by a clinical variable | Multivariate Cox regression including RNA-seq, copy number, and pathology | Session info

Installation | Citing curatedTCGAData | Data versions | Version 2.0.1 | Data source | Downloading datasets | Caveats for working with TCGA data | ACC dataset example | Subtype information | Typical clinical variables | Identifying samples in Assays | Separating samples | TCGAprimaryTumors convenience | Keeping colData in an extracted Assay | Example use of RaggedExperiment | Exporting Data | Session Information | References

Installation | Citing curatedTCGAData | Data versions | Version 2.0.1 | Data source | Downloading datasets | Caveats for working with TCGA data | ACC dataset example | Subtype information | Typical clinical variables | Identifying samples in Assays | Separating samples | TCGAprimaryTumors convenience | Keeping colData in an extracted Assay | Example use of RaggedExperiment | Exporting Data | Session Information | References

Loading | Overview | Data from the cBioPortal API (cBioPortalData()) | Packaged data from cBioDataPack() | sessionInfo

Installation | Introduction | Overview | API representation | Operations | Searching through the API | Studies | Clinical Data | Molecular Profiles | Molecular Profile Data | Genes | All available genes | Gene Panels | Molecular Gene Panels | genePanelMolecular | getGenePanelMolecular | getDataByGenes | Samples | Sample List Identifiers | Sample Identifiers | All samples within a study ID | Info on Samples | Advanced Usage | Clearing the cache | sessionInfo

Installation | Introduction | Citations | Overview | Data Structures | Identifying available studies | Choosing download method | Two main functions | cBioDataPack: Obtain Study Data as Zipped Tarballs | cBioPortalData: Obtain data from the cBioPortal API | Considerations | metadata | Build prompts | Manual downloads | Clearing the cache | cBioDataPack | cBioPortalData | Example Analysis: Kaplan-Meier Plot | Data update requests | sessionInfo | References

Introduction | Loading the package | Discovering studies | cBioPortalData setup | cgdsr setup | Obtaining Cases | cBioPortalData (Cases) | Notes | sampleLists | samples from sampleLists | getSampleInfo | cgdsr (Cases) | getCaseLists and getClinicalData | Obtaining Clinical Data | cBioPortalData (Clinical) | All clinical data | By sample data | cgdsr (Clinical) | getClinicalData | Clinical Data Summary | Molecular or Genetic Profiles | cBioPortalData (molecularProfiles) | cgdsr (getGeneticProfiles) | Genomic Profile Data for a set of genes | cBioPortalData (Indentify samples and genes) | Convert hugoGeneSymbol to entrezGeneId | Obtain all samples in study | cgdsr (Profile Data) | Molecular Data with cBioPortalData | molecularData | getDataByGenes | cBioPortalData: the main end-user function | Mutation Data | cBioPortalData (mutationData) | cgdsr (getMutationData) | Copy Number Alteration (CNA) | cBioPortalData (CNA) | cgdsr (CNA) | Methylation Data | cBioPortalData (Methylation) | cgdsr (Methylation) | sessionInfo

Loading | Overview | Data from the cBioPortal API (cBioPortalData()) | Packaged data from cBioDataPack() | sessionInfo

Installation | Introduction | Overview | API representation | Operations | Searching through the API | Studies | Clinical Data | Molecular Profiles | Molecular Profile Data | Genes | All available genes | Gene Panels | Molecular Gene Panels | genePanelMolecular | getGenePanelMolecular | getDataByGenes | Samples | Sample List Identifiers | Sample Identifiers | All samples within a study ID | Info on Samples | Advanced Usage | Clearing the cache | sessionInfo

Installation | Introduction | Citations | Overview | Data Structures | Identifying available studies | Choosing download method | Two main functions | cBioDataPack: Obtain Study Data as Zipped Tarballs | cBioPortalData: Obtain data from the cBioPortal API | Considerations | metadata | Build prompts | Manual downloads | Clearing the cache | cBioDataPack | cBioPortalData | Example Analysis: Kaplan-Meier Plot | Data update requests | sessionInfo | References

Introduction | Loading the package | Discovering studies | cBioPortalData setup | cgdsr setup | Obtaining Cases | cBioPortalData (Cases) | Notes | sampleLists | samples from sampleLists | getSampleInfo | cgdsr (Cases) | getCaseLists and getClinicalData | Obtaining Clinical Data | cBioPortalData (Clinical) | All clinical data | By sample data | cgdsr (Clinical) | getClinicalData | Clinical Data Summary | Molecular or Genetic Profiles | cBioPortalData (molecularProfiles) | cgdsr (getGeneticProfiles) | Genomic Profile Data for a set of genes | cBioPortalData (Indentify samples and genes) | Convert hugoGeneSymbol to entrezGeneId | Obtain all samples in study | cgdsr (Profile Data) | Molecular Data with cBioPortalData | molecularData | getDataByGenes | cBioPortalData: the main end-user function | Mutation Data | cBioPortalData (mutationData) | cgdsr (getMutationData) | Copy Number Alteration (CNA) | cBioPortalData (CNA) | cgdsr (CNA) | Methylation Data | cBioPortalData (Methylation) | cgdsr (Methylation) | sessionInfo

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 | 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 | 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

Overview | Installation | curatedTCGAData utility functions | obtaining TCGA as MultiAssayExperiment objects from curatedTCGAData | sampleTables: what sample types are present in the data? | TCGAsplitAssays: separate the data from different tissue types | getSubtypeMap: manually curated molecular subtypes | getClinicalNames: key "level 4" clinical & pathological data | Converting Assays to SummarizedExperiment | CpGtoRanges | qreduceTCGA | symbolsToRanges | Importing TCGA text data files to Bioconductor classes | Work around for long file names on Windows | makeGRangesListFromCopyNumber | makeSummarizedExperimentFromGISTIC | mergeColData: expanding the colData of a MultiAssayExperiment | Translating and interpreting TCGA identifiers | GDC Data Updates | UUID History Lookup | Translation | TCGA barcode to UUID | UUID to TCGA barcode | UUID to UUID | Parsing TCGA barcodes | Sample selection | Primary tumors | data.frame representation of barcode | OncoPrint - oncoPrintTCGA | Reference data | sampleTypes | clinicalNames - Firehose pipeline clinical variables | sessionInfo

Overview | Installation | curatedTCGAData utility functions | obtaining TCGA as MultiAssayExperiment objects from curatedTCGAData | sampleTables: what sample types are present in the data? | TCGAsplitAssays: separate the data from different tissue types | getSubtypeMap: manually curated molecular subtypes | getClinicalNames: key "level 4" clinical & pathological data | Converting Assays to SummarizedExperiment | CpGtoRanges | qreduceTCGA | symbolsToRanges | Importing TCGA text data files to Bioconductor classes | Work around for long file names on Windows | makeGRangesListFromCopyNumber | makeSummarizedExperimentFromGISTIC | mergeColData: expanding the colData of a MultiAssayExperiment | Translating and interpreting TCGA identifiers | GDC Data Updates | UUID History Lookup | Translation | TCGA barcode to UUID | UUID to TCGA barcode | UUID to UUID | Parsing TCGA barcodes | Sample selection | Primary tumors | data.frame representation of barcode | OncoPrint - oncoPrintTCGA | Reference data | sampleTypes | clinicalNames - Firehose pipeline clinical variables | sessionInfo

Installation | Load | G&T-seq: parallel sequencing data of single-cell genomes and transcriptomes | Downloading datasets | Obtaining the data | Exploring the data structure | Copy numbers | RNA-seq | sessionInfo | References

Installation | Load | Description | Downloading datasets | Exploring the data structure | Cell metadata | RNA expression | Chromatin Accessibility | Suggested software for the downstream analysis | sessionInfo

Installation | Load packages | scNMT: single-cell nucleosome, methylation and transcription sequencing | Dataset lookup | Data versions | Downloading the data | Checking the cell metadata | Exploring the data structure | Chromatin Accessibility (acc_*) | DNA Methylation (met_*) | sessionInfo | References

Installation | Load packages | SCoPE2 | Downloading data sets | Available projects | Retrieving data | The macrophage differentiation project | Data versions | Cell annotation | Transcriptomic data | Proteomic data | sessionInfo | References

Installation | Load | G&T-seq: parallel sequencing data of single-cell genomes and transcriptomes | Downloading datasets | Obtaining the data | Exploring the data structure | Copy numbers | RNA-seq | sessionInfo | References

Installation | Load | Description | Downloading datasets | Exploring the data structure | Cell metadata | RNA expression | Chromatin Accessibility | Suggested software for the downstream analysis | sessionInfo

Installation | Load packages | scNMT: single-cell nucleosome, methylation and transcription sequencing | Dataset lookup | Data versions | Downloading the data | Checking the cell metadata | Exploring the data structure | Chromatin Accessibility (acc_*) | DNA Methylation (met_*) | sessionInfo | References

Installation | Load packages | SCoPE2 | Downloading data sets | Available projects | Retrieving data | The macrophage differentiation project | Data versions | Cell annotation | Transcriptomic data | Proteomic data | sessionInfo | References

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

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

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

oncoKBData | Installation | Package Load | Introduction | API representation | Operations | Levels of Evidence | Gene tables | Session Information

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

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

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

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

Installation | Load libraries | ECCITE-seq dataset | Downloading datasets | Exploring the data structure | scRNA-seq data | scADT data | CTCL/CTRL conditions | sgRNAs CRISPR pertubation data | SingleCellExperiment object conversion | Session Info | Additional References | References

Installation | Load libraries | ECCITE-seq dataset | Downloading datasets | Exploring the data structure | scRNA-seq data | scADT data | CTCL/CTRL conditions | sgRNAs CRISPR pertubation data | SingleCellExperiment object conversion | Session Info | Additional References | References

Installation | Load libraries | CITE-seq dataset | Downloading datasets | Exploring the data structure | scRNA-seq data | scADT data | SingleCellExperiment object conversion | Session Info | References

Installation | Load packages | seq-FISH dataset | Downloading datasets | Exploring the data structure | Visualize matching cell identifiers across assays | scRNA-seq data | seq-FISH data | Other data version | Data version 1.0.0 | Session Info

SingleCellMultiModal | Overview | Installation | Loading packages | Citing SingleCellMultiModal | Representation | Contributions | Further resources | References

Installation | Load libraries | CITE-seq dataset | Downloading datasets | Exploring the data structure | scRNA-seq data | scADT data | SingleCellExperiment object conversion | Session Info | References

Installation | Load packages | seq-FISH dataset | Downloading datasets | Exploring the data structure | Visualize matching cell identifiers across assays | scRNA-seq data | seq-FISH data | Other data version | Data version 1.0.0 | Session Info

SingleCellMultiModal | Overview | Installation | Loading packages | Citing SingleCellMultiModal | Representation | Contributions | Further resources | References

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

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

Introduction & installation | Query and pivot | Select, filter and transform with j_query() | Array-of-objects to R data.frame with j_pivot() | NDJSON support | R objects as input | Patch | Applying a patch with j_patch_apply() | Difference between documents with j_patch_from() | Schema validation | Flatten and find | The JSON parser | Using jsonlite::fromJSON() | C++ library use in other packages | Session information

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?

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

Flushing the Software Repository | Check the Day's Report | Comment Out Software Propagation in the Crontab | Make a Backup | Remove All Packages | Rerun the postrun.sh | Manually Run updateReposPkgs-bioc.sh | Uncomment Software Propagation in the Crontab

Introduction | Installation | Data Client | Example Dataset | Conversion to Bioconductor classes | Raw Data | Session Info | References

Introduction | Installation | Data Client | Example Dataset | Conversion to Bioconductor classes | Raw Data | Session Info | References