Codelink statistics

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Citations per year

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

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

This word cloud represents Codelink usage per disease context
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Popular tool citations

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Protocols

Codelink specifications

Information


Unique identifier OMICS_15016
Name Codelink
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.48.0
Stability Stable
Requirements
limma, methods, parallel, R(>=2.10), knitr, genefilter, annotate, Biobase(>=2.17.8), BiocGenerics(>=0.3.2)
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Diego Diez

Publication for Codelink

Codelink citations

 (21)
library_books

Identification of differentially expressed genes and signaling pathways in ovarian cancer by integrated bioinformatics analysis

2018
PMCID: 5858852
PMID: 29588600
DOI: 10.2147/OTT.S152238

[…] fferent probe sequences of the same target DNA. There are various platforms available (http://arrayconsortium.tgen. org/np2/home.do; http://www1.amershambiosciences.com/APTR1X/upp01077.nsf/Contentand/codelink_bioarray_system; http://www.affymetrix.com; http://www.illumina.com/prod_expression.htm; and http://www.nimblegen.com; http://www.xeotron.com).Using the keywords “ovarian cancer geo accession […]

library_books

Gene Expression Analysis Reveals Novel Shared Gene Signatures and Candidate Molecular Mechanisms between Pemphigus and Systemic Lupus Erythematosus in CD4+ T Cells

2018
Front Immunol
PMCID: 5776326
PMID: 29387060
DOI: 10.3389/fimmu.2017.01992

[…] till produced biased results (Figure ), the raw files were preprocessed again and an additional normalization step was performed. In detail, raw gene expression profiles were deduced from text files (Codelink array) using Codelink R package (). Using the same package, first, the background was corrected with the “normexp” method and then normalized by the “cyclicloess” method. For Affymetrix data, […]

library_books

Robust RNAi enhancement via human Argonaute 2 overexpression from plasmids, viral vectors and cell lines

2013
Nucleic Acids Res
PMCID: 3834839
PMID: 24049077
DOI: 10.1093/nar/gkt836

[…] ny) and hybridized on the microarray. miCHIP is based on locked nucleic acid (LNA) technology, whereby LNA-modified Tm-normalized miRCURY capture probes (Exiqon, Denmark, miRBase v11) were printed on Codelink slides (GE Healthcare, Munich, Germany). Microarray images were generated using the Genepix 4200AL laser scanner (Molecular Devices, Biberach an der Riss, Germany) in batches using the Genepi […]

library_books

Systematic review of genome wide gene expression studies of bipolar disorder

2013
PMCID: 3765828
PMID: 23945090
DOI: 10.1186/1471-244X-13-213

[…] verwhelming majority of the 25 studies on the brain were carried out with Affymetrix array platforms. Thirteen were carried out with the U133A or U133 Plus 2.0, seven on U95AV2, three on cDNA, one on Codelink, and one on Agilent arrays. […]

call_split

Gene Expression Patterns of Hemizygous and Heterozygous KIT Mutations Suggest Distinct Oncogenic Pathways: A Study in NIH3T3 Cell Lines and GIST Samples

2013
PLoS One
PMCID: 3625162
PMID: 23593401
DOI: 10.1371/journal.pone.0061103
call_split See protocol

[…] Codelink® Whole Mouse Genome Bioarrays (GE/Amersham) of one sample of WT, D6, D54, WT/D6, WT/D54 and MIGR NIH3T3 cells cultivated in the three different conditions SCF+, SCF− and imatinib were used fo […]

call_split

Testing for Differentially Expressed MicroRNAs with Errors in Variables Nonparametric Regression

2012
PLoS One
PMCID: 3360044
PMID: 22655055
DOI: 10.1371/journal.pone.0037537
call_split See protocol

[…] om R package affy can be used to perform the quantile normalization . The traditional LOESS normalization method is based on the idea of the versus plot, which has been implemented in an R packages codelink and affy , . The LOESS-M normalization is a modification of the traditional loess normalization by subtracting the median of from the loess fit to the MA-plot . R functions were written to […]


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Codelink institution(s)
Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, Madrid, Spain; Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
Codelink funding source(s)
Supported by the Programa I3P de la Red de Bioinformática del CSIC (pre-doctoral fellowship), Comunidad de Madrid 08.5/0042/2003 and GR/SAL/0382/2004, MEC BFI2002- 00489 y Red de Centros RCMN (C03/08).

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