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Citations per year

Number of citations per year for the bioinformatics software tool lumi
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Tool usage distribution map

This map represents all the scientific publications referring to lumi per scientific context
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Associated diseases

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Popular tool citations

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Protocols

lumi specifications

Information


Unique identifier OMICS_00770
Name lumi
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.32.0
Stability Stable
Requirements
AnnotationDbi, limma, methods, stats, RColorBrewer, graphics, GenomicRanges, stats4, lattice, R(>=2.10), GenomicFeatures, preprocessCore, MASS, genefilter, Biobase(>=2.5.5), vsn, affy(>=1.23.4), methylumi(>=2.3.2), annotate, mgcv(>=1.4-0), nleqslv, KernSmooth, RSQLite, DBI, beadarray, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping
Maintained Yes

Versioning


No version available

Documentation


Publications for lumi

lumi citations

 (221)
call_split

Integrative multi platform meta analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers

2018
PLoS One
PMCID: 5884535
PMID: 29617451
DOI: 10.1371/journal.pone.0194844
call_split See protocol

[…] ray Average (RMA) analysis from the Bio-conductor R package oligo []. In the same way, Illumina expression data (Cohort 2) was pre-processed by applying Quantile Normalization (QN) from the R package lumi []. In both cases, genes with low variability expression values were discarded to reduce false-positive rates.Data from both platforms were integrated with the virtualArray software R package []. […]

library_books

Altered DNA methylation in liver and adipose tissues derived from individuals with obesity and type 2 diabetes

2018
BMC Med Genet
PMCID: 5822594
PMID: 29466957
DOI: 10.1186/s12881-018-0542-8

[…] Computation and statistical analyses were performed using the R, version 3.1 (http://www.r-project.org). The Lumi package was used to normalize the raw intensities of DNA methylation and gene expression arrays (robust spline normalization) []. Then, Beta as well as log2 transformed gene expression values wer […]

library_books

Hypomethylation of CYP2E1 and DUSP22 Promoters Associated With Disease Activity and Erosive Disease Among Rheumatoid Arthritis Patients

2018
PMCID: 5876118
PMID: 29287311
DOI: 10.1002/art.40408

[…] al, we retained 428,232 CpG sites in 229 samples (58 CD14+ monocyte samples, 57 CD19+ B cell samples, 56 CD4+ naive T cell samples, and 58 CD4+ memory T cell samples). Statistical analysis. Using the Lumi R package , , methylation β values were transformed to M values in order to better approximate the homoscedasticity assumption in most statistical analyses. For each RA clinical outcome, robust l […]

library_books

A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome

2018
Sci Rep
PMCID: 5790004
PMID: 29382850
DOI: 10.1038/s41598-017-17919-5

[…] t. The bioinformatic analyses were performed at the SciLife Lab, Department of Medical Biochemistry and Microbiology, Uppsala, Sweden. Data were background corrected and quantile normalized using the Lumi package. The Oligo package from Bioconductor was used to compute Robust Multichip average expression measures. Probes were filtered based on mean detection p–value ≤0.05. […]

library_books

The transcription factors Runx3 and ThPOK cross regulate acquisition of cytotoxic function by human Th1 lymphocytes

2018
eLife
PMCID: 5844691
PMID: 29488879
DOI: 10.7554/eLife.30496.036

[…] Raw data were quantile normalized using the normalization method from the lumi package (). Unsupervised clustering (Uc) analysis of gene expression datasets was performed using the pvclust package of the R software (R)(). The robustness of the Uc tree was tested by multisca […]

library_books

Use of deep neural network ensembles to identify embryonic fetal transition markers: repression of COX7A1 in embryonic and cancer cells

2017
Oncotarget
PMCID: 5814259
PMID: 29487692
DOI: 10.18632/oncotarget.23748

[…] ive fluorescence units (RFUs) were considered as nonspecific background signal. Raw microarray data were normalized with the R BeadArray library. Analysis of microarray data was performed using the R lumi library. […]


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lumi institution(s)
Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA

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