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.
Last updated 1 months ago
infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073
14.81 score 70 stars 126 dependents 670 scripts 9.2k 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 6 days ago
infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073
12.95 score 70 stars 125 dependents 670 scriptscBioPortalData - 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 6 days ago
softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073
10.09 score 33 stars 4 dependents 148 scripts 644 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 12 days ago
softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073
10.06 score 31 stars 4 dependents 148 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.
Last updated 1 months ago
softwareworkflowsteppreprocessingdataimportbioconductor-packagetcgau24ca289073utilities
9.56 score 24 stars 8 dependents 203 scripts 1.3k 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.
Last updated 1 months ago
softwareworkflowsteppreprocessingdataimportbioconductor-packagetcgau24ca289073utilities
9.45 score 24 stars 8 dependents 203 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).
Last updated 1 months ago
softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-package
8.89 score 51 stars 1 dependents 58 scripts 913 downloadscuratedTCGAData - 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.
Last updated 2 months ago
homo_sapiens_datareproducibleresearchcancerdataexperimenthubbioconductor-package
7.71 score 44 stars 1 dependents 184 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>.
Last updated 2 months ago
experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073
7.27 score 17 stars 57 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.
Last updated 3 months ago
immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwritingbioconductor-package
6.55 score 13 stars 23 scripts 237 downloadsbugsigdbr - 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.
Last updated 3 months ago
dataimportgenesetenrichmentmetagenomicsmicrobiomebioconductor-package
6.51 score 3 stars 48 scripts 201 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.
Last updated 3 months ago
copynumbervariationdifferentialexpressiongeneexpressiongenomewideassociationgenomicvariationmicroarrayrnaseqsnpbioconductor-package
5.87 score 7 stars 10 scripts 214 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.
Last updated 2 months ago
softwareinfrastructuredataimportsinglecellbioconductor-package
5.62 score 2 dependents 7 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.
Last updated 2 months ago
softwareinfrastructuredataimportsinglecellbioconductor-packageu24ca289073
5.59 score 2 dependents 7 scripts 137 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.
Last updated 22 days ago
softwareinfrastructuredataimportsinglecellspatialbioconductor-packagegenomics
4.85 score 11 scripts 104 downloadsterraTCGAdata - 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.
Last updated 3 months ago
softwareinfrastructuredataimportbioconductor-package
4.60 score 4 scripts 187 downloadsterraTCGAdata - 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.
Last updated 3 months ago
softwareinfrastructuredataimportbioconductor-package
4.60 score 4 scriptsMicrobiomeBenchmarkData - 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.
Last updated 3 months ago
experimentdatamicrobiomedatareproducibleresearchsequencingdatabioconductor-package
4.39 score 18 scripts