MultiAssayExperiment - Software for the integration of multi-omics experiments in Bioconductor
Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.
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infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073
15.00 score 75 stars 146 dependents 920 scripts 9.7k downloadsTCGAutils - TCGA utility functions for data management
A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.
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softwareworkflowsteppreprocessingdataimportbioconductor-packagetcgau24ca289073utilities
10.26 score 29 stars 11 dependents 267 scripts 2.2k downloadscBioPortalData - Exposes and Makes Available Data from the cBioPortal Web Resources
The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations.
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softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073
10.23 score 34 stars 4 dependents 254 scripts 836 downloadscBioPortalData - Exposes and Makes Available Data from the cBioPortal Web Resources
The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations.
Last updated
softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073
10.22 score 34 stars 4 dependents 253 scriptsTCGAutils - TCGA utility functions for data management
A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.
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softwareworkflowsteppreprocessingdataimportbioconductor-packagetcgau24ca289073utilities
9.93 score 29 stars 11 dependents 267 scriptsGSEABase - Gene set enrichment data structures and methods
This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
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geneexpressiongenesetenrichmentgraphandnetworkgokegg
8.83 score 75 dependents 2.5k scriptslefser - R implementation of the LEfSE method for microbiome biomarker discovery
lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).
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softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-packager01ca230551
8.56 score 66 stars 110 scripts 1.2k downloadslefser - R implementation of the LEfSE method for microbiome biomarker discovery
lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).
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softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-packager01ca230551
8.46 score 65 stars 110 scriptscuratedTCGAData - Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.
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homo_sapiens_datareproducibleresearchcancerdataexperimenthubbioconductor-packageu24ca289073
7.89 score 44 stars 1 dependents 277 scriptsSingleCellMultiModal - Integrating Multi-modal Single Cell Experiment datasets
SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see <https://doi.org/10.1371/journal.pcbi.1011324>.
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experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073
7.48 score 18 stars 88 scriptscuratedMetagenomicData - Curated Metagenomic Data of the Human Microbiome
The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects.
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experimenthubhomo_sapiens_datamicrobiomedatareproducibleresearchbioconductorbioconductor-packager01ca230551
7.37 score 154 stars 380 scriptsbugsigdbr - R-side access to published microbial signatures from BugSigDB
The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.
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dataimportgenesetenrichmentmetagenomicsmicrobiomebioconductor-packager01ca230551
6.98 score 6 stars 67 scriptsGSEABenchmarkeR - Reproducible GSEA Benchmarking
The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated.
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immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwritingbioconductor-packageu24ca289073
6.95 score 14 stars 30 scripts 373 downloadsimageTCGAutils - Utility functions for working with histopathology images
Utility functions for working with CONCH data, listing remote files. One function assigns HoverNet nuclei to ProvGigaPath tiles with a scale factor to align coordinates. Provides internal utility functions for 'imageFeatureTCGA' and most functions are not meant for end users.
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softwareworkflowsteppreprocessing
5.22 score 2 scripts 211 downloadsMultiAssayExperiment - Software for the integration of multi-omics experiments in Bioconductor
Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.
Last updated
infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073
13.27 score 75 stars 145 dependents 1.7k scriptsbugsigdbr - R-side access to published microbial signatures from BugSigDB
The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.
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dataimportgenesetenrichmentmetagenomicsmicrobiomebioconductor-packager01ca230551
6.98 score 6 stars 67 scripts 854 downloadsVisiumIO - Import Visium data from the 10X Space Ranger pipeline
The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.
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softwareinfrastructuredataimportsinglecellspatialbioconductor-packagegenomicsu24ca289073
6.84 score 3 stars 1 dependents 95 scripts 326 downloadsVisiumIO - Import Visium data from the 10X Space Ranger pipeline
The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.
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softwareinfrastructuredataimportsinglecellspatialbioconductor-packagegenomicsu24ca289073
6.84 score 3 stars 1 dependents 95 scriptsdoppelgangR - Identify likely duplicate samples from genomic or meta-data
The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).
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immunooncologyrnaseqmicroarraygeneexpressionqualitycontrolbioconductor-package
6.69 score 5 stars 33 scriptsGSEABenchmarkeR - Reproducible GSEA Benchmarking
The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated.
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immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwritingbioconductor-packageu24ca289073
6.64 score 14 stars 30 scriptsTENxIO - Import methods for 10X Genomics files
Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.
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softwareinfrastructuredataimportsinglecellbioconductor-packageu24ca289073
6.16 score 1 stars 5 dependents 16 scripts 408 downloadsTENxIO - Import methods for 10X Genomics files
Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.
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softwareinfrastructuredataimportsinglecellbioconductor-packageu24ca289073
6.16 score 1 stars 5 dependents 16 scriptsimageFeatureTCGA - Import features from hovernet, provgigapath into a MultiAssayExperiment
The package imports data from HoverNet, and ProvGigaPath pipelines. Pipeline output data are hosted in a self-owned online repository. Package functionality conveniently incorporates pipeline data into existing MultiAssayExperiment instances from curatedTCGAData.
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softwareinfrastructuredataimportdatarepresentation
6.11 score 1 stars 1 dependents 13 scripts 223 downloadsCNVRanger - Summarization and expression/phenotype association of CNV ranges
The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.
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copynumbervariationdifferentialexpressiongeneexpressiongenomewideassociationgenomicvariationmicroarrayrnaseqsnpbioconductor-packageu24ca289073
5.86 score 8 stars 13 scripts 401 downloadsHMP16SData - 16S rRNA Sequencing Data from the Human Microbiome Project
HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.
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experimentdataexperimenthubhomo_sapiens_datamicrobiomedatareproducibleresearchsequencingdatabioconductorbioconductor-packagehmpr01ca230551
5.67 score 10 stars 45 scriptsbugphyzz - A harmonized data resource and software for enrichment analysis of microbial physiologies
bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods.
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microbiomedatareproducibleresearchr01ca230551
5.43 score 6 stars 32 scriptsHistoImagePlot - Plotting functionality for Histopathology pipeline datasets
Create side-by-side visualizations of tissue thumbnail image and HoverNet cell segmentation with colored cell type labels. Functionality automatically retrieves the thumbnail image associated with a HoverNet JSON file and overlays the segmentation data. This package is intended for researchers working with histopathological images, facilitating exploratory analysis, and integrates with the imageFeatureTCGA Bioconductor package.
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softwarevisualizationspatial
4.88 score 2 scripts 251 downloadsXeniumIO - Import and represent Xenium data from the 10X Xenium Analyzer
The package allows users to readily import spatial data obtained from the 10X Xenium Analyzer pipeline. Supported formats include 'parquet', 'h5', and 'mtx' files. The package mainly represents data as SpatialExperiment objects.
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softwareinfrastructuredataimportsinglecellspatialu24ca289073
4.70 score 3 scriptsterraTCGAdata - OpenAccess TCGA Data on Terra as MultiAssayExperiment
Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.
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softwareinfrastructuredataimportbioconductor-packageu24hg010263
4.60 score 5 scriptsterraTCGAdata - OpenAccess TCGA Data on Terra as MultiAssayExperiment
Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.
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softwareinfrastructuredataimportbioconductor-packageu24hg010263
4.60 score 4 scripts 290 downloadsMicrobiomeBenchmarkData - Datasets for benchmarking in microbiome research
The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.
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experimentdatamicrobiomedatareproducibleresearchsequencingdatabioconductor-packager01ca230551
4.28 score 21 scriptsbedbaser - A BEDbase client
A client for BEDbase. bedbaser provides access to the API at api.bedbase.org. It also includes convenience functions to import BED files into GRanges objects and BEDsets into GRangesLists.
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softwaredataimportthirdpartyclientu24ca289073
4.22 score 3 stars 4 scriptsbedbaser - A BEDbase client
A client for BEDbase. bedbaser provides access to the API at api.bedbase.org. It also includes convenience functions to import BED files into GRanges objects and BEDsets into GRangesLists.
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softwaredataimportthirdpartyclientu24ca289073
4.22 score 3 stars 4 scripts 279 downloadsXeniumIO - Import and represent Xenium data from the 10X Xenium Analyzer
The package allows users to readily import spatial data obtained from the 10X Xenium Analyzer pipeline. Supported formats include 'parquet', 'h5', and 'mtx' files. The package mainly represents data as SpatialExperiment objects.
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softwareinfrastructuredataimportsinglecellspatialu24ca289073
3.70 score 3 scripts 228 downloads