imageFeatureTCGA | Installation | Introduction | Importing HoverNet JSON Data | From Local Files | Import the H5ad file into a SpatialExperiment | Basic Overlay | Customized Overlay | Custom Color Palette | Visualizing Additional Features | Session Info

Introduction | Installation | Loading packages | Import Prov-GigaPath tile level embeddings | Embedding PCA | Spatial Patterns | Adding HoverNet Nuclei Features | Visualizing Hovernet nuclei vs tile coordinates to see that they do not match | Scale factor between nuclei coordinates and tile coordinates | Session Info | References

imageFeatureTCGA | Overview | Installation | Data structure and technical details | HoVerNet outputs | ProvGigaPath embeddings | Slide-level embeddings | Tile-level embeddings | Available Data | Formats | HoVerNet data | ProvGigaPath data | Importing HoVerNet data | Importing ProvGigaPath embeddings | Importing multiple ProvGigaPath files | Mixed level imports | See also | Shiny App: imageTCGA | Session Info

BugSigDB: a comprehensive database of published microbial signatures | Obtaining published microbial signatures from BugSigDB | Extracting microbe signatures | Writing microbe signatures to file in GMT format | Displaying BugSigDB signature and taxon pages | Ontology-based queries for experimental factors and body sites | Session info

BugSigDB: a comprehensive database of published microbial signatures | Obtaining published microbial signatures from BugSigDB | Extracting microbe signatures | Writing microbe signatures to file in GMT format | Displaying BugSigDB signature and taxon pages | Ontology-based queries for experimental factors and body sites | Session info

Introduction | Supported Formats | TENxIO | VisiumIO | XeniumIO | Installation | Loading package | Example Folder Structure | Xenium class | import method | Importing an Example Xenium Dataset | Session Info

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

Introduction | Data types | Case Study: Batch correction in Japanese datasets | Important options | Changing sensitivity | Use of the ExpressionSet | Parallelizing | Caching

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

Overview | Background | Install and load pacakge | Citing lefser | Analysis example | Prepare input | Terminal node | Relative abundance | Run lefser | Visualization using lefserPlot | Benchmarking against other tools | Interoperating with phyloseq | Session Info

Overview | Background | Install and load pacakge | Citing lefser | Analysis example | Prepare input | Terminal node | Relative abundance | Run lefser | Visualization using lefserPlot | Benchmarking against other tools | Interoperating with phyloseq | Session Info

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

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

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

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

Introduction | Applicability and Scope | Key functions | Reading and accessing CNV data | Input data format | Representation as a GRangesList | Representation as a RaggedExperiment | Summarizing individual CNV calls across a population | Trimming low-density areas | Reciprocal overlap | Identifying recurrent regions | Overlap analysis of CNVs with functional genomic regions | Finding and illustrating overlaps | Overlap permutation test | CNV-expression association analysis | Application to individual CNV and RNA-seq assays | Application to TCGA data stored in a MultiAssayExperiment | CNV-phenotype association analysis | Setting up a CNV-GWAS | Running a CNV-GWAS | Producing a GDS file in advance | Using relative signal intensities | Session info | 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

Import data | Ids of the spike-in bacteria | Recalibrate based on Salinibacter ruber abundance. | A more convenient way using the scml function included in the package: | Session information

Introduction | Data schema | Analysis and Stats | Installation | Import bugphyzz data | Create microbial signatures | Run a bug set enrichment analysis | Get signatures associated with a specific microbe | Session information

GeneSet | GeneColorSet | GeneSetCollection

Introduction | Installation | Sample metadata | Accessing datasets | Print avaialable datasets | Access a single dataset | Access a few datasets | Access all of the datasets | Annotations for each taxa are included in rowData | Cache | Session information

Purpose of the package | Setup | Expression data sources | Microarray compendium | RNA-seq compendium | User-defined data compendium | Differential expression | Enrichment analysis | User-defined enrichment methods | Benchmarking | Runtime | Fraction of significant gene sets | Phenotype relevance | MalaCards disease relevance rankings | Mapping between dataset ID and disease code | Relevance score of a gene set ranking | Random relevance score distribution | Theoretical optimum | Cross-dataset relevance score distribution | User-defined relevance rankings | Advanced | Caching | Parallel computation

Purpose of the package | Setup | Expression data sources | Microarray compendium | RNA-seq compendium | User-defined data compendium | Differential expression | Enrichment analysis | User-defined enrichment methods | Benchmarking | Runtime | Fraction of significant gene sets | Phenotype relevance | MalaCards disease relevance rankings | Mapping between dataset ID and disease code | Relevance score of a gene set ranking | Random relevance score distribution | Theoretical optimum | Cross-dataset relevance score distribution | User-defined relevance rankings | Advanced | Caching | Parallel computation

Publications | Prerequisites | Introduction | Features | Frequency Table Generation | Straightforward Subsetting | HMP Controlled-Access Participant Data | Apply for dbGaP Access | Install the SRA Toolkit | Merge with HMP16SData | Analysis Using the phyloseq Package | Coercion to phyloseq Objects | Alpha Diversity Analysis | Beta Diversity Analysis | Principle Coordinates Analysis | Phylum-level Comparison to Metagenomic Shotgun Sequencing | Exporting Data to CSV, SAS, SPSS, and STATA Formats | Prepare Data for Export | Export to CSV Format | Export to SAS Format | Export to SPSS Format | Export to STATA Format | Session Information