rhdf5 - R Interface to HDF5
This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.
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infrastructuredataimportbioconductorhdf5rhdf5curlopensslcpp
14.43 score 74 stars 293 dependents 5.9k scripts
biomaRt - Interface to BioMart databases (i.e. Ensembl)
In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<https://www.ensembl.org/info/data/biomart/index.html>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintained by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.
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annotationbioconductorbiomartensembl
12.53 score 52 stars 233 dependents 16k scriptsRarr - A Simple and Performant Native R Reader & Writer for Zarr Arrays
The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. Its design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on an external tools or libraries.
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dataimportbioconductorome-ngffome-zarron-diskout-of-memoryzarrc-blosclibzstd
11.00 score 55 stars 9 dependents 96 scripts
Rhdf5lib - hdf5 library as an R package
Provides C and C++ hdf5 libraries.
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infrastructurebioconductorhdf5hdf5-library
10.06 score 7 stars 416 dependents 34 scripts
rhdf5filters - HDF5 Compression Filters
Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seamless integration with rhdf5, however the compiled filters can also be used with external applications.
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infrastructuredataimportcompressionfilter-pluginhdf5
8.93 score 5 stars 294 dependents 12 scriptsbeadarray - Quality assessment and low-level analysis for Illumina BeadArray data
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
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microarrayonechannelqualitycontrolpreprocessing
8.73 score 6 dependents 93 scripts 1.8k downloadsarrayQualityMetrics - Quality metrics report for microarray data sets
This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.
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microarrayqualitycontrolonechanneltwochannelreportwritingbioconductor
7.63 score 1 stars 1 dependents 338 scriptsFITfileR - Read FIT files using only native R code
The 'FIT' (Flexible and Interoperable Data Transfer) protocol is designed specifically for sharing data from fitness and health devices. This package allows reading 'FIT' files in pure R without any dependence on external software or SDKs.
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fitfitfilegarmin
5.38 score 72 stars 66 scriptsBiocWorkflowTools - Tools to aid the development of Bioconductor Workflow packages
Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.
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softwarereportwriting
5.03 score 1 dependents 12 scripts 552 downloadsBeadDataPackR - Compression of Illumina BeadArray data
Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.
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microarray
5.02 score 7 dependents 2 scriptsBeadDataPackR - Compression of Illumina BeadArray data
Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.
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microarray
4.94 score 7 dependents 1.0k downloadsmsmbstyle - MSMB Styles for R Markdown Documents
Provides R Markdown output formats to use with Modern Statistics for Modern Biology.
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bookdownrmarkdown-template
3.48 score 60 stars 4 scriptsminionSummaryData - Summarised MinION sequencing data published by Ashton et al. 2015
Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects.
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experimentdatasequencingdatadatapkg
3.30 score 2 scriptsIONiseR - Quality Assessment Tools for Oxford Nanopore MinION data
IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.
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qualitycontroldataimportsequencing
2.40 score 5 scriptsBeadArrayUseCases - Analysing Illumina BeadArray expression data using Bioconductor
Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor
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microarraydatadatapkg
2.30 score 2 scripts