BiocManager - Access the Bioconductor Project Package Repository
A convenient tool to install and update Bioconductor packages.
Last updated 2 months ago
core-services
16.47 score 74 stars 414 dependents 2.9k scripts 249k downloadsBiocManager - Access the Bioconductor Project Package Repository
A convenient tool to install and update Bioconductor packages.
Last updated 2 months ago
core-services
16.47 score 74 stars 414 dependents 2.9k scripts 249k 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 2 months ago
infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073
14.94 score 71 stars 126 dependents 670 scripts 9.1k 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 2 months ago
infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcgau24ca289073
13.02 score 71 stars 127 dependents 670 scriptsGenomicDataCommons - NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
Last updated 2 months ago
dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette
10.78 score 87 stars 12 dependents 238 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 end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.
Last updated 1 months ago
infrastructure
10.41 score 8 stars 11 dependents 248 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()`.
Last updated 4 months ago
annotationdataimportbioconductor-packagecore-package
10.20 score 1 stars 492 dependents 19 scripts 31k 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 13 days ago
softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073
10.17 score 33 stars 4 dependents 147 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 3 months ago
softwareinfrastructurethirdpartyclientbioconductor-packagenci-itcru24ca289073
10.06 score 31 stars 4 dependents 148 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.
Last updated 1 months ago
infrastructurebioconductor-packagecore-services
10.03 score 8 stars 6 dependents 114 scripts 3.4k downloadsRTCGAToolbox - 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.
Last updated 4 months ago
differentialexpressiongeneexpressionsequencing
9.75 score 18 stars 5 dependents 76 scripts 810 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 4 months ago
softwareworkflowsteppreprocessingdataimportbioconductor-packagetcgau24ca289073utilities
9.66 score 27 stars 10 dependents 210 scripts 1.5k downloadsBiocCheck - 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.
Last updated 1 months ago
infrastructurebioconductor-packagecore-services
9.50 score 8 stars 6 dependents 115 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 4 months ago
softwareworkflowsteppreprocessingdataimportbioconductor-packagetcgau24ca289073utilities
9.49 score 27 stars 10 dependents 210 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.
Last updated 4 months ago
infrastructuredatarepresentationcopynumbercore-packagedata-structuremutationsu24ca289073
8.93 score 4 stars 14 dependents 76 scripts 1.4k downloadsAnVIL - 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 end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.
Last updated 1 months ago
infrastructure
8.85 score 11 dependents 250 scripts 1.1k downloadsRaggedExperiment - 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.
Last updated 4 months ago
infrastructuredatarepresentationcopynumbercore-packagedata-structuremutationsu24ca289073
8.79 score 4 stars 14 dependents 76 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.
Last updated 4 months ago
differentialexpressiongeneexpressionsequencing
8.75 score 18 stars 5 dependents 76 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()`.
Last updated 4 months ago
annotationdataimportbioconductor-packagecore-package
8.70 score 1 stars 492 dependents 19 scriptsBiocBaseUtils - General utility functions for developing Bioconductor packages
The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.
Last updated 5 months ago
softwareinfrastructurebioconductor-packagecore-package
8.68 score 4 stars 159 dependents 3 scripts 10.0k 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.
Last updated 3 months ago
annotationinfrastructuregokeggbiocartabioconductor-packagecore-package
8.48 score 5 stars 4 dependents 167 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.
Last updated 3 months ago
annotationinfrastructuregokeggbiocartabioconductor-packagecore-package
8.48 score 5 stars 4 dependents 167 scripts 784 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.
Last updated 6 months ago
apiopenapiswagger
8.07 score 68 stars 13 dependents 32 scripts 762 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.
Last updated 6 months ago
apiopenapiswagger
8.06 score 66 stars 13 dependents 32 scripts 698 downloadsBiocBaseUtils - General utility functions for developing Bioconductor packages
The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.
Last updated 5 months ago
softwareinfrastructurebioconductor-packagecore-package
7.68 score 4 stars 158 dependents 3 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.
Last updated 30 days ago
softwareinfrastructurebioconductormetadatau24ca289073
7.65 score 21 stars 66 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 4 months ago
experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073
7.29 score 17 stars 60 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 4 months ago
experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073
7.29 score 17 stars 60 scriptsrjsoncons - 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.
Last updated 7 months ago
cpp
7.08 score 9 stars 9 dependents 8 scripts 859 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.
Last updated 5 months ago
softwareinfrastructure
6.50 score 19 dependents 70 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.
Last updated 5 months ago
softwareinfrastructure
6.45 score 19 dependents 70 scripts 253 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 4 months ago
softwareinfrastructuredataimportsinglecellbioconductor-packageu24ca289073
5.80 score 3 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 4 months ago
softwareinfrastructuredataimportsinglecellbioconductor-packageu24ca289073
5.77 score 3 dependents 7 scripts 213 downloadsAnVILGCP - 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 work with the AnVIL package. User-level interaction with this package should be minimal.
Last updated 2 months ago
softwareinfrastructurethirdpartyclientdataimport
5.59 score 3 dependents 27 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 work with the AnVIL package. User-level interaction with this package should be minimal.
Last updated 2 months ago
softwareinfrastructurethirdpartyclientdataimport
5.56 score 3 dependents 27 scripts 151 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 2 months ago
softwareinfrastructuredataimportsinglecellspatialbioconductor-packagegenomicsu24ca289073
5.50 score 1 dependents 14 scripts 134 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 2 months ago
softwareinfrastructuredataimportsinglecellspatialbioconductor-packagegenomicsu24ca289073
5.50 score 1 dependents 14 scriptsAnVILAz - 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.
Last updated 5 months ago
softwareinfrastructurethirdpartyclient
5.30 score 5 scriptsAnVILAz - 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.
Last updated 5 months ago
softwareinfrastructurethirdpartyclient
5.30 score 5 scripts 137 downloadsAnVILPublish - 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.
Last updated 5 months ago
infrastructuresoftware
5.26 scoreterraTCGAdata - 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 5 months ago
softwareinfrastructuredataimportbioconductor-package
4.60 score 4 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.
Last updated 5 months ago
softwareinfrastructuredataimportbioconductor-package
4.60 score 4 scripts 245 downloadsAnVILPublish - 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.
Last updated 5 months ago
infrastructuresoftware
4.48 score 236 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.
Last updated 2 months ago
softwareinfrastructuredataimportsinglecellspatialu24ca289073
4.40 score 2 scripts 96 downloadsReleaseLaunch - 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.
Last updated 3 days ago
4.16 scoreBiocHubsShiny - 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.
Last updated 29 days ago
softwareshinyapps
3.90 score 1 scripts 182 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.
Last updated 29 days ago
softwareshinyapps
3.90 score 1 scriptsoncoKBData - 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.
Last updated 6 months ago
infrastructurethirdpartyclientu24ca289073
2.00 score 1 stars 2 scriptsBiocCertificate - Generate Conference Certificates
A shiny app to generate conference certificates and letters from templates. The interactive app allows the user to enter their name and generate a PDF file for download. The app uses rmarkdown to render PDF certificates and letters with the default pdflatex engine.
Last updated 7 months ago
2.00 scoreBranchRename - Utilities for renaming branches on GitHub
The package provides utility functions at the user and organization level for renaming branches on GitHub. The functions are written mainly for modifying batches of either repositories or packages. It uses tools to authenticate and call git from within R.
Last updated 7 months ago
2.00 score 3 scriptsnewsfeed - Compilies NEWS files from different packages
The package takes NEWS files from other packages and puts them into a single file
Last updated 6 months ago
1.70 score 2 scriptsOncoTree - Expose the OncoTree API for R
Expose the OncoTree API for R. OncoTree is a standardized ontology of cancer terms that is used to annotate cancer data. This package provides a set of functions to query the OncoTree API and retrieve information about cancer types, subtypes, and their relationships.
Last updated 12 months ago
1.28 score 19 scripts