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Oligo package specifications

Information


Unique identifier OMICS_14343
Name Oligo package
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format CEL, XYS
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements
limma, methods, stats, RColorBrewer, graphics, splines, utils, R(>=2.11.0), genefilter, pd.mapping50k.xba240, oligoClasses(>=1.9.41), affyio(>=1.15.2), affxparser(>=1.17.3), Biobase(>=2.7.3), DBI(>=0.2-4), preprocessCore(>=1.9.0), hapmap100kxba, pd.hg18.60mer.expr, maqcExpression4plex
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Benilton Carvalho <>

Publication for Oligo package

Oligo package citations

 (49)
library_books

Deconvolution of Human Brain Cell Type Transcriptomes Unraveled Microglia Specific Potential Biomarkers

2018
PMCID: 5932158
PMID: 29755398
DOI: 10.3389/fneur.2018.00266

[…] microarray affy hugene-2_0-st data (gse78115) (). specifically, we considered the 12 samples (3 replicates each) derived from 2 different cell lines ncrm-5 and inc-01 of ipsc origin. using oligo package of r bioconductor, we performed data analysis (including data normalization) to assess the differential expression pattern specific to human microglia with respect to ipscs. the oligo […]

library_books

LRH 1 agonism favours an immune islet dialogue which protects against diabetes mellitus

2018
PMCID: 5902555
PMID: 29662071
DOI: 10.1038/s41467-018-03943-0

[…] was applied on a per-chip basis for background correction. subsequent normalization across arrays, and summarization were performed using a quantile algorithm and median-polish, respectively, via oligo package from bioconductor (http://www.bioconductor.org). a differential gene expression analysis was then performed using the limma package. computed p values were corrected using the false […]

library_books

Decipher reliable biomarkers of brain aging by integrating literature based evidence with interactome data

2018
PMCID: 5938059
PMID: 29651153
DOI: 10.1038/s12276-018-0057-6

[…] and functionally overlap in the context of the interactome., expression data (gse46706) of post-mortem brain tissue from individuals aged 16–102 were downloaded, processed, and normalized using the oligo package. we implemented weighted correlation network analysis (wgcna) to identify co-expression modules reflecting aging-specific expression patterns in the brain. each module was annotated […]

library_books

Macrophage Derived Extracellular Succinate Licenses Neural Stem Cells to Suppress Chronic Neuroinflammation

2018
PMCID: 5842147
PMID: 29478844
DOI: 10.1016/j.stem.2018.01.020

[…] (https://www.bioconductor.org/packages/release/bioc/html/pdinfobuilder.html) using the platform files provided by affymetrix. the cel files were then loaded into r, rma normalized with the oligo package, and filtered to only retain probes annotated as “main” (). differential expression testing was performed using limma () and the resulting p.values were corrected […]

library_books

Screening for key lncRNAs in the progression of gallbladder cancer using bioinformatics analyses

2018
PMCID: 5928615
PMID: 29512694
DOI: 10.3892/mmr.2018.8655

[…] of the gpl16686 affymetrix human gene 2.0 st array (affymetrix inc., santa clara, ca, usa) for further analysis., all the raw data were preprocessed using the robust multichip average method in the oligo package (available through bioconductor version 3.0; http://www.bioconductor.org) (). the comparison of differentially expressed lncrnas and mrnas in separate gbc tissues with normal tissues […]

library_books

A 65 gene signature for prognostic prediction in colon adenocarcinoma

2018
PMCID: 5810222
PMID: 29393333
DOI: 10.3892/ijmm.2018.3401

[…] containing 56 tumor samples and 55 matched normal samples from patients with colon tumors. the data in the gse44861 dataset was subject to background correction and normalization using the oligo package () in r language., the limma package in r language was used to screen degs between tumor samples and normal samples in tcga and gse44861 datasets. the false discovery rate (fdr) […]


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Oligo package institution(s)
Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
Oligo package funding source(s)
Doctoral scholarship awarded by the Brazilian Funding Agency CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) and National Institutes of Health grants R01RR021967 and P41HG004059.

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