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Ringo specifications

Information


Unique identifier OMICS_00809
Name Ringo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.44.0
Stability Stable
Requirements
limma, methods, RColorBrewer, grid, Matrix, stats4, lattice, genefilter, vsn, mclust, Biobase(>=1.14.1), BiocGenerics(>=0.1.11), rtracklayer(>=1.3.1), topGO(>=1.15.0)
Maintained Yes

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Documentation


Publication for Ringo

Ringo in publications

 (3)
PMCID: 5659820
PMID: 28949289
DOI: 10.7554/eLife.28590.019

[…] was extracted from the scanned image files and processed using the r package (). probe intensities were transformed from raw values into background-corrected normalized log ratios (chip/input) using ringo's preprocess method (vsn normalization). smoothing over individual probe intensities was performed using a sliding window of 1000 bp along the chromosome and replacing the intensity […]

PMCID: 4860964
PMID: 27462442
DOI: 10.1038/celldisc.2015.45

[…] intensity files from the geo data set gse30204 were imported into r (ver. 2.11.1), and the log2 enrichments (log2 bound/input ratios) for each individual probe were calculated using the package ringo []. the arrays were loess-normalized using the normalizewithinarrays function of the limma package. for each promoter, we calculated the average log2 enrichment values using data obtained […]

PMCID: 3091638
PMID: 20642838
DOI: 10.1186/1471-2164-11-441

[…] lowess spatial normalisation []. further data analysis was carried out by the authors. data from roche nimblegen was analysed with r [] using bioconductor []. data was parsed to r with the package ringo [] and snapcgh []. as the use of variance stabilizing normalisation (vsn) [] alone was unable to completely remove colour biases from the data (data not shown), the data was first normalised […]


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Ringo institution(s)
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Ringo funding source(s)
This work was supported by the European Union (FP6 HeartRepair 018630).

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