minfi protocols

minfi specifications


Unique identifier OMICS_00799
Name minfi
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
Stability Stable
Maintained Yes



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Publication for minfi

minfi IN pipelines

PMCID: 5428306
PMID: 28325913
DOI: 10.1038/s41598-017-00384-5

[…] nucleated cells isolated from cord blood (leukocytes and nucleated red blood cells)66 and an adult leukocyte reference panel for blood samples collected in early or mid-childhood as implemented in minfi 58, 67. we conducted a principal component analysis in the resulting 384,349 cpgs across all cord blood samples and used univariate linear regression models to explore associations among […]

PMCID: 5603607
PMID: 28924151
DOI: 10.1038/s41598-017-12084-1

[…] the 485,577 cpg sites was calculated as the ratio of methylated signal divided by the sum of methylated and unmethylated signals plus 100. to avoid batch effects, the function preprocessfunnorm in minfi package was used38. it is particularly useful for studies comparing conditions with known large-scale differences, such as cancer/normal studies, or between-tissue studies. it has been shown […]

PMCID: 4312439
PMID: 25623364
DOI: 10.1186/s12967-015-0384-5

[…] infinium humanmethylation450 beadchip kit (illumina). instead of using illumina's genomestudio software, raw idat files were obtained and further preprocessed using the r/bioconductorminfi package [minfi]. red and green channel intensities were obtained from the raw idat files. detection p-values for each probe were also computed and used in order to discard those probes with low quality. […]

PMCID: 3777004
PMID: 23982603
DOI: 10.1038/bjc.2013.496

[…] of samples, which make use of detection p-values, are available in r and bioconductor packages, such as the preprocessing and analysis pipeline (touleimat and tost, 2012), ima (wang et al, 2012), minfi (hansen and aryee, 2013) and methylumi (davis et al, 2011)., similar to sample quality control, it is customary to filter probes if a certain proportion of samples (i.e., >25%) […]

minfi institution(s)
Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Biostatistics, Johns Hopkins School of Public Health, Baltimore, MD, USA; Lieber Institute of Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA, Department of Computer Science, University of Maryland, College Park, MD, USA, Department of Epidemiology, USA, Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

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