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 25 days ago

infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073

14.98 score 70 stars 128 dependents 670 scripts 9.2k downloads

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 15 days ago

infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073

13.01 score 70 stars 126 dependents 670 scripts

cBioPortalData - 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 11 days ago

softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073

10.12 score 33 stars 4 dependents 147 scripts 644 downloads

cBioPortalData - 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 2 months ago

softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073

10.06 score 31 stars 4 dependents 148 scripts

TCGAutils - 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 2 months ago

softwareworkflowsteppreprocessingdataimportbioconductor-packagetcgau24ca289073utilities

9.68 score 26 stars 10 dependents 210 scripts 1.4k downloads

TCGAutils - 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 2 months ago

softwareworkflowsteppreprocessingdataimportbioconductor-packagetcgau24ca289073utilities

9.54 score 26 stars 10 dependents 210 scripts

lefser - 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 4 days ago

softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-package

8.47 score 55 stars 56 scripts 913 downloads

SingleCellMultiModal - 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 3 months ago

experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073

7.29 score 17 stars 60 scripts

GSEABenchmarkeR - 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 4 months ago

immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwritingbioconductor-packageu24ca289073

6.55 score 13 stars 23 scripts 282 downloads

bugsigdbr - 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 4 months ago

dataimportgenesetenrichmentmetagenomicsmicrobiomebioconductor-package

6.46 score 3 stars 48 scripts 257 downloads

CNVRanger - 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 4 months ago

copynumbervariationdifferentialexpressiongeneexpressiongenomewideassociationgenomicvariationmicroarrayrnaseqsnpbioconductor-packageu24ca289073

5.69 score 7 stars 10 scripts 260 downloads

TENxIO - 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 3 months ago

softwareinfrastructuredataimportsinglecellbioconductor-packageu24ca289073

5.62 score 2 dependents 7 scripts

TENxIO - 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 3 months ago

softwareinfrastructuredataimportsinglecellbioconductor-packageu24ca289073

5.59 score 2 dependents 7 scripts 216 downloads

VisiumIO - 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 11 days ago

softwareinfrastructuredataimportsinglecellspatialbioconductor-packagegenomicsu24ca289073

5.02 score 14 scripts 130 downloads

terraTCGAdata - 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 4 months ago

softwareinfrastructuredataimportbioconductor-package

4.60 score 4 scripts 236 downloads

terraTCGAdata - 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 4 months ago

softwareinfrastructuredataimportbioconductor-package

4.60 score 4 scripts

XeniumIO - 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.

Last updated 11 days ago

softwareinfrastructuredataimportsinglecellspatialu24ca289073

4.40 score 2 scripts 5 downloads

MicrobiomeBenchmarkData - 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 4 months ago

experimentdatamicrobiomedatareproducibleresearchsequencingdatabioconductor-package

4.39 score 18 scripts

bedbaser - 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.

Last updated 24 days ago

softwaredataimportthirdpartyclientu24ca289073

4.02 score 1 stars 3 scripts 9 downloads