GEOquery - Get data from NCBI Gene Expression Omnibus (GEO)

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

Last updated 27 days ago

microarraydataimportonechanneltwochannelsagebioconductorbioinformaticsdata-sciencegenomicsncbi-geo

13.64 score 88 stars 54 packages 4.3k scripts 15k downloads

GenomicDataCommons - NIH / NCI Genomic Data Commons Access

Programmatically access the NIH / NCI Genomic Data Commons RESTful service.

Last updated 27 days ago

dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette

11.67 score 84 stars 10 packages 181 scripts 1.6k downloads

methylumi - Handle Illumina methylation data

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

Last updated 27 days ago

dnamethylationtwochannelpreprocessingqualitycontrolcpgisland

10.07 score 8 stars 16 packages 83 scripts 2.6k downloads

BiocPkgTools - 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 23 days ago

softwareinfrastructurebioconductormetadata

7.83 score 19 stars 69 scripts 468 downloads

ACME - Algorithms for Calculating Microarray Enrichment (ACME)

ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

Last updated 27 days ago

technologymicroarraynormalization

3.30 score 4 scripts 388 downloads