Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

By Martin J. Aryee, Andrew E. Jaffe, Héctor Corrada Bravo, Christine Ladd-Acosta, Andrew P. Feinberg, Kasper D. Hansen, Rafael A. Irizarry. Bioinform., 2014

3,850 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e71f1c7012a7605ab8fafe4d2520c8d9f63376e3

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In Molecular Biology

Citations in the corpus

Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma (2017, positive): “Data were preprocessed using the “minfi” (73) and “wateRmelon” (74) R packages.”
eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data (2016, methodology): “We used the dmpFinder function in minfi (Aryee et al., 2014) to make an initial call of tissue-specific methylation differences.”
Epigenetic Signatures of Cigarette Smoking (2016, neutral): “Likewise, there is strong support in the literature for PRRT132 and TNF.33 The enrichment results for methylation platform coverage also yielded the same 3 genes.”
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions (2018, methodology): “minfi (11), a widely used pipeline for Infinium array processing (1), calculates the P-values in a similar parametric way, but with the M and U probes combined into one foreground signal and one”
RnBeads 2.0: comprehensive analysis of DNA methylation data (2019, methodology): “…memory consumption with other software packages for DNA methylation microarray analysis highlighted in a recent review paper [54], namely minfi [37], methylumi (http://bioconductor.org/packages/release/bioc/html/methylumi.html), watermelon [38], and ChAMP [39], and with the methyKit [40]…”
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease (2016, methodology): “Data cleaning procedures were undertaken using R package “minfi” [69], generating quality control report, finding sample outliers, cell counts estimation, and annotation accessing.”
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells (2016, background): “…3.2 Foissac and Sammeth, 2007; Monlong et al., 2014 http://sammeth.net/confluence/display/ASTA/2+-+Download Minfi Aryee et al., 2014 https://bioconductor.org/packages/release/bioc/html/minfi.html NOOB Triche et al., 2013…”
A computational solution for bolstering reliability of epigenetic clocks: Implications for clinical trials and longitudinal tracking (2021, methodology): “36.0) 52 .”
DNA methylation age of blood predicts all-cause mortality in later life (2015, neutral): “was used to generate methylation beta values [39].”
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi (2016, methodology): “The minﬁ package in R/Bioconductor (Gentleman et al., 2004; Huber et al., 2015) is a widely used software package for analyzing data from the Illumina HumanMethyla-tion450 array (Aryee et al., 2014).”