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.

Last updated 24 days ago

infrastructuredataimporthdf5rhdf5opensslcurlzlibcpp

16.14 score 61 stars 232 dependents 4.2k scripts 35k downloads

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 (<http://www.biomart.org>). 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 maintain 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.

Last updated 3 days ago

annotationbioconductorbiomartensembl

15.92 score 38 stars 231 dependents 13k scripts 38k downloads

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.

Last updated 24 days ago

infrastructuredataimporthdf5rhdf5opensslcurlzlibcpp

13.74 score 61 stars 232 dependents 4.2k 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 (<http://www.biomart.org>). 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 maintain 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.

Last updated 3 days ago

annotationbioconductorbiomartensembl

13.34 score 38 stars 231 dependents 13k scripts

Rhdf5lib - hdf5 library as an R package

Provides C and C++ hdf5 libraries.

Last updated 3 months ago

infrastructurebioconductorhdf5hdf5-libraryfortranzlib

11.32 score 6 stars 341 dependents 26 scripts 41k downloads

rhdf5filters - HDF5 Compression Filters

Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seemless integration with rhdf5, however the compiled filters can also be used with external applications.

Last updated 3 months ago

infrastructuredataimportcompressionfilter-pluginhdf5

9.84 score 5 stars 232 dependents 4 scripts 33k downloads

Rhdf5lib - hdf5 library as an R package

Provides C and C++ hdf5 libraries.

Last updated 10 months ago

infrastructurebioconductorhdf5hdf5-libraryfortranzlib

9.41 score 6 stars 341 dependents 26 scripts

rhdf5filters - HDF5 Compression Filters

Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seemless integration with rhdf5, however the compiled filters can also be used with external applications.

Last updated 10 months ago

infrastructuredataimportcompressionfilter-pluginhdf5

8.15 score 5 stars 234 dependents 4 scripts

beadarray - 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.

Last updated 3 months ago

microarrayonechannelqualitycontrolpreprocessing

6.83 score 4 dependents 70 scripts

Rarr - Read Zarr Files in R

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It's design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specifcation in R with minimal reliance on an external tools or libraries.

Last updated 1 days ago

dataimportome-zarron-diskout-of-memoryzarrc-blosclibzstd

6.59 score 34 stars 21 scripts

Rarr - Read Zarr Files in R

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It's design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specifcation in R with minimal reliance on an external tools or libraries.

Last updated 2 months ago

dataimportome-zarron-diskout-of-memoryzarrc-blosclibzstd

6.55 score 34 stars 21 scripts 272 downloads

arrayQualityMetrics - 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.

Last updated 3 months ago

microarrayqualitycontrolonechanneltwochannelreportwriting

5.98 score 1 stars 193 scripts 956 downloads

FITfileR - 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.

Last updated 3 days ago

fitfitfilegarmin

5.59 score 56 stars 46 scripts

BeadDataPackR - Compression of Illumina BeadArray data

Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

Last updated 9 months ago

microarray

4.88 score 5 dependents 2 scripts

BeadDataPackR - Compression of Illumina BeadArray data

Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

Last updated 3 months ago

microarray

4.78 score 5 dependents 2 scripts 910 downloads

arrayQualityMetrics - 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.

Last updated 6 years ago

microarrayqualitycontrolonechanneltwochannelreportwriting

4.68 score 1 stars 193 scripts

IONiseR - 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.

Last updated 4 years ago

qualitycontroldataimportsequencing

4.40 score 5 scripts

BiocWorkflowTools - 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.

Last updated 3 months ago

softwarereportwriting

4.30 score 10 scripts 482 downloads

IONiseR - 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.

Last updated 3 months ago

qualitycontroldataimportsequencing

4.30 score 5 scripts 366 downloads

msmbstyle - MSMB Styles for R Markdown Documents

Provides R Markdown output formats to use with Modern Statistics for Modern Biology.

Last updated 3 years ago

bookdownrmarkdown-template

3.47 score 59 stars 4 scripts