BiocManager - Access the Bioconductor Project Package Repository
The Bioconductor project publishes packages on a six-month release cycle. This package is a convenient tool to install and update Bioconductor packages. For more information about Bioconductor, see <https://bioconductor.org>.
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core-services
16.19 score 76 stars 425 dependents 4.6k scripts 266k downloadsBiocManager - Access the Bioconductor Project Package Repository
The Bioconductor project publishes packages on a six-month release cycle. This package is a convenient tool to install and update Bioconductor packages. For more information about Bioconductor, see <https://bioconductor.org>.
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core-services
16.19 score 76 stars 425 dependents 4.6k scripts 266k 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.
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infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073
15.00 score 75 stars 146 dependents 920 scripts 9.7k 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.
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infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073
13.14 score 75 stars 145 dependents 1.3k scriptsAnVIL - Bioconductor on the AnVIL compute environment
The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides programatic access to the Dockstore, Leonardo, Rawls, TDR, and Terra RESTful programming interfaces. For platform-specific user-level functionality, see either the AnVILGCP or AnVILAz package.
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infrastructureu24hg010263
10.48 score 7 stars 12 dependents 306 scriptsGenomicDataCommons - NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
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dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette
10.42 score 90 stars 13 dependents 277 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.
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softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073
10.32 score 35 stars 4 dependents 308 scriptsAnVIL - Bioconductor on the AnVIL compute environment
The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides programatic access to the Dockstore, Leonardo, Rawls, TDR, and Terra RESTful programming interfaces. For platform-specific user-level functionality, see either the AnVILGCP or AnVILAz package.
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infrastructureu24hg010263
10.18 score 7 stars 12 dependents 311 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
9.94 score 31 stars 11 dependents 259 scriptsBiocCheck - Bioconductor-specific package checks
BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.
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infrastructurebioconductor-packagecore-services
9.76 score 10 stars 6 dependents 134 scriptsBiocCheck - Bioconductor-specific package checks
BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.
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infrastructurebioconductor-packagecore-services
9.76 score 10 stars 6 dependents 128 scriptsRTCGAToolbox - A new tool for exporting TCGA Firehose data
Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.
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differentialexpressiongeneexpressionsequencing
9.70 score 19 stars 5 dependents 106 scriptsBiocBaseUtils - Utility and internal functions for Bioconductor packages
The package coalesces typical helper functions that are scattered throughout the Bioconductor ecosystem. It aims to reduce code redundancy by formalizing functions often used by Bioconductor developers. These functions include operations such as replacing slots in an object, selecting observations for show methods, labeling function life cycles, and more.
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softwareinfrastructurebioconductor-packagecore-package
9.38 score 4 stars 713 dependents 7 scripts 11k downloadsUniProt.ws - R Interface to UniProt Web Services
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. This package provides a collection of functions for retrieving, processing, and re-packaging UniProt web services. The package makes use of UniProt's modernized REST API and allows mapping of identifiers accross different databases.
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annotationinfrastructuregokeggbiocartabioconductor-packagecore-package
8.98 score 10 stars 6 dependents 266 scriptsUniProt.ws - R Interface to UniProt Web Services
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. This package provides a collection of functions for retrieving, processing, and re-packaging UniProt web services. The package makes use of UniProt's modernized REST API and allows mapping of identifiers accross different databases.
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annotationinfrastructuregokeggbiocartabioconductor-packagecore-package
8.97 score 10 stars 6 dependents 261 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
8.94 score 31 stars 11 dependents 259 scriptsRaggedExperiment - Representation of Sparse Experiments and Assays Across Samples
This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.
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infrastructuredatarepresentationcopynumbercore-packagedata-structuremutationsu24ca289073
8.71 score 5 stars 14 dependents 102 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.
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softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073
8.67 score 35 stars 4 dependents 308 scriptsRaggedExperiment - Representation of Sparse Experiments and Assays Across Samples
This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.
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infrastructuredatarepresentationcopynumbercore-packagedata-structuremutationsu24ca289073
8.61 score 5 stars 14 dependents 107 scriptsBiocIO - Standard Input and Output for Bioconductor Packages
The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.
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annotationdataimportbioconductor-packagecore-package
8.60 score 1 stars 524 dependents 42 scriptsBiocIO - Standard Input and Output for Bioconductor Packages
The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.
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annotationdataimportbioconductor-packagecore-package
8.52 score 1 stars 515 dependents 36 scriptsBiocBaseUtils - Utility and internal functions for Bioconductor packages
The package coalesces typical helper functions that are scattered throughout the Bioconductor ecosystem. It aims to reduce code redundancy by formalizing functions often used by Bioconductor developers. These functions include operations such as replacing slots in an object, selecting observations for show methods, labeling function life cycles, and more.
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softwareinfrastructurebioconductor-packagecore-package
8.33 score 4 stars 709 dependents 3 scriptsRTCGAToolbox - A new tool for exporting TCGA Firehose data
Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.
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differentialexpressiongeneexpressionsequencing
8.22 score 19 stars 5 dependents 106 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
8.03 score 45 stars 1 dependents 283 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
8.03 score 45 stars 1 dependents 283 scriptsBiocPkgTools - Collection of simple tools for learning about Bioconductor Packages
Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.
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softwareinfrastructurebioconductormetadatau24ca289073
7.85 score 22 stars 1 dependents 119 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
7.49 score 19 stars 102 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
7.47 score 18 stars 102 scriptsrapiclient - Dynamic OpenAPI/Swagger Client
Access services specified in OpenAPI (formerly Swagger) format. It is not a code generator. Client is generated dynamically as a list of R functions.
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apiopenapiswagger
7.43 score 67 stars 14 dependents 39 scripts 1.2k downloadsrapiclient - Dynamic OpenAPI/Swagger Client
Access services specified in OpenAPI (formerly Swagger) format. It is not a code generator. Client is generated dynamically as a list of R functions.
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apiopenapiswagger
7.39 score 67 stars 14 dependents 39 scripts 1.1k 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
6.89 score 3 stars 1 dependents 109 scriptsVisiumIO - 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 400 downloadsrjsoncons - Query, Pivot, Patch, and Validate 'JSON' and 'NDJSON'
Functions to query (filter or transform), pivot (convert from array-of-objects to object-of-arrays, for easy import as 'R' data frame), search, patch (edit), and validate (against 'JSON Schema') 'JSON' and 'NDJSON' strings, files, or URLs. Query and pivot support 'JSONpointer', 'JSONpath' or 'JMESpath' expressions. The implementation uses the 'jsoncons' <https://danielaparker.github.io/jsoncons/> header-only library; the library is easily linked to other packages for direct access to 'C++' functionality not implemented here.
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cpp
6.51 score 8 stars 14 dependents 9 scripts 1.9k downloadsAnVILBase - Generic functions for interacting with the AnVIL ecosystem
Provides generic functions for interacting with the AnVIL ecosystem. Packages that use either GCP or Azure in AnVIL are built on top of AnVILBase. Extension packages will provide methods for interacting with other cloud providers.
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softwareinfrastructureu24hg010263
6.20 score 17 dependents 77 scriptsAnVILBase - Generic functions for interacting with the AnVIL ecosystem
Provides generic functions for interacting with the AnVIL ecosystem. Packages that use either GCP or Azure in AnVIL are built on top of AnVILBase. Extension packages will provide methods for interacting with other cloud providers.
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softwareinfrastructureu24hg010263
6.20 score 17 dependents 77 scripts 768 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
6.10 score 1 stars 5 dependents 14 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
6.08 score 1 stars 5 dependents 16 scriptsAnVILGCP - The GCP R Client for the AnVIL
The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to use the API calls from the AnVIL package. It coordinates AnVIL workspace functionality with native GCP tools.
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softwareinfrastructurethirdpartyclientdataimportu24hg010263
5.81 score 5 dependents 39 scriptsGCPtools - Tools for working with gcloud and gsutil
Lower-level functionality to interface with Google Cloud Platform tools. 'gcloud' and 'gsutil' are both supported. The functionality provided centers around utilities for the AnVIL platform.
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softwareinfrastructurethirdpartyclientdataimportbioconductor-packageu24hg010263
5.77 score 15 dependents 22 scriptsAnVILGCP - The GCP R Client for the AnVIL
The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to use the API calls from the AnVIL package. It coordinates AnVIL workspace functionality with native GCP tools.
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softwareinfrastructurethirdpartyclientdataimportu24hg010263
5.71 score 5 dependents 38 scriptsAnVILPublish - Publish Packages and Other Resources to AnVIL Workspaces
Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the 'DASHBOARD'. Vignettes are translated to python notebooks ready for evaluation in AnVIL.
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infrastructuresoftwareu24hg010263
5.65 score 1 dependents 2 scriptsAnVILPublish - Publish Packages and Other Resources to AnVIL Workspaces
Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the 'DASHBOARD'. Vignettes are translated to python notebooks ready for evaluation in AnVIL.
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infrastructuresoftwareu24hg010263
5.65 score 1 dependents 2 scripts 316 downloadsAnVILAz - R / Bioconductor Support for the AnVIL Azure Platform
The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVILAz package supports end-users and developers using the AnVIL platform in the Azure cloud. The package provides a programmatic interface to AnVIL resources, including workspaces, notebooks, tables, and workflows. The package also provides utilities for managing resources, including copying files to and from Azure Blob Storage, and creating shared access signatures (SAS) for secure access to Azure resources.
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softwareinfrastructurethirdpartyclientu24hg010263
5.08 score 5 scripts 254 downloadsAnVILAz - R / Bioconductor Support for the AnVIL Azure Platform
The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVILAz package supports end-users and developers using the AnVIL platform in the Azure cloud. The package provides a programmatic interface to AnVIL resources, including workspaces, notebooks, tables, and workflows. The package also provides utilities for managing resources, including copying files to and from Azure Blob Storage, and creating shared access signatures (SAS) for secure access to Azure resources.
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softwareinfrastructurethirdpartyclientu24hg010263
5.08 score 5 scriptsshinybiocloader - Use a Shiny Bioconductor CSS loader
Add a Bioconductor themed CSS loader to your shiny app. It is based on the shinycustomloader R package. Use a spinning Bioconductor note loader to enhance your shiny app loading screen. This package is intended for developer use.
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softwareinfrastructureguibioconductor-packagequarto
5.08 score 2 dependents 5 scripts 207 downloadsBiocPkgDash - An interactive Shiny dashboard for Bioconductor package maintainers
This package provides an interactive Shiny dashboard for Bioconductor package maintainers. It visualizes various package statuses, metadata, and development metrics, offering insights into package health and activity. This tool aims to support maintainers of multiple packages by filtering packages via maintainer email.
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softwareinfrastructurevisualizationguiu24ca289073
4.88 score 4 scripts 108 downloadsBiocPkgDash - An interactive Shiny dashboard for Bioconductor package maintainers
This package provides an interactive Shiny dashboard for Bioconductor package maintainers. It visualizes various package statuses, metadata, and development metrics, offering insights into package health and activity. This tool aims to support maintainers of multiple packages by filtering packages via maintainer email.
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softwareinfrastructurevisualizationguiu24ca289073
4.81 score 4 scriptsBiocAzul - Programmatic Access to the Azul API
Represents the OpenAPI v2 Azul API as an R object for performing requests. The infrastructure uses the AnVIL and rapiclient packages. Users can connect to either the AnVIL or Human Cell Atlas Data Explorers.
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softwareinfrastructuredataimportthirdpartyclientu24hg010263
4.70 score 2 scripts 150 downloadsAnVILVRS - Expose the vrs_anvil_toolkit Python package via R
Process Variant Call Format (VCF) files and perform lookup operations on Genomic Variation Representation Service (GA4GH VRS) identifiers. The GA4GH VRS identifiers provide a standardized way to represent genomic variations, making it easier to exchange and share genomic information.
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softwarebiologicalquestionvariantannotationinfrastructurethirdpartyclientu24hg010263
4.70 score 2 scripts 80 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.
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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 downloadsBiocHubsShiny - View AnnotationHub and ExperimentHub Resources Interactively
A package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package.
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softwareshinyapps
4.30 score 3 scriptsBiocHubsShiny - View AnnotationHub and ExperimentHub Resources Interactively
A package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package.
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softwareshinyapps
4.30 score 3 scriptsReleaseLaunch - R utilities related to Bioconductor release tasks
The package faciliates a Bioconductor release. It currently updates existing Bioconductor repositories on GitHub after a release. The script creates the RELEASE_XX_YY branch and pushes it to the Bioconductor organization.
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4.05 score 2 scriptsXeniumIO - 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 downloadsoncoKBData - A package to access the oncoKB web API
It provides access to the oncoKB API using the rapiclient and AnVIL R / Bioconductor packages. It allows access to both public and private APIs. Private API access requires a token obtained from https://www.oncokb.org.
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infrastructurethirdpartyclientu24ca289073
2.70 score 1 stars 2 scripts