oneChannelGUI protocols

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oneChannelGUI specifications

Information


Unique identifier OMICS_02004
Name oneChannelGUI
Software type Pipeline/Workflow
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
Version 1.28.6
Stability Stable
Requirements
Biobase, IRanges, Biostrings, siggenes, affylmGUI, tkWidgets, Rsamtools(>=1.13.1), chimera
Maintained Yes

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Maintainer


  • person_outline Raffaele A. Calogero <>

Publication for oneChannelGUI

oneChannelGUI in pipelines

 (3)
2013
PMCID: 3595110
PMID: 23555082
DOI: 10.1155/2013/340620

[…] hd, running linux suse enterprise 11. statistics and data parsing were executed using r scripting, taking advantage of bioconductor [] packages, that is, biostrings, org.hs.eg.db, genomicranges, and onechannelgui []., fusionmap developers provide a synthetic dataset of simulated paired-end rna-seq reads (~60,000 pairs of reads, 75 nt, fragment size = 158 bp). fifty fusions are represented […]

2013
PMCID: 3633050
PMID: 23815381
DOI: 10.1186/1471-2105-14-S7-S2

[…] using r scripting, taking advantage of the gplots-contributed r package http://cran.r-project.org/web/packages/gplots/ and bioconductor [] packages, i.e. biostrings, org.hs.eg.db, genomicranges and onechannelgui []., the negative dataset was generated using beers []http://www.cbil.upenn.edu/beers/, consisting of 70 million 100 paired-end reads (parameters: -readlength 100 -tlen 5 -tpercent […]

2013
PMCID: 3876710
PMID: 24453408
DOI: 10.1155/2013/137629

[…] at 45°c for 17 hours. the arrays were washed and stained in affymetrix fluidics station 450 and scanned using the affymetrix genechip scanner 3000., the microarray experiments were analyzed with the onechannelgui package available in r software. the signal intensities from each chip were preliminarily normalized with rma method and filtered by iqr filter choosing as threshold a value of 0.25. […]


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oneChannelGUI in publications

 (35)
PMCID: 5839389
PMID: 29515758
DOI: 10.18632/oncotarget.22709

[…] using the robust multichip average (rma) method []. fold-change and statistic parameters of sicontrol versus sitdrd9-1 or sitdrd9-2 comparisons were performed using the limma package [] through onechannelgui []. genes differentially expressed more than 2-fold (lineal change) and with fdr < 0.01 were selected. genes that were differentially expressed with both sirnas that target tdrd9 […]

PMCID: 5494305
PMID: 28658625
DOI: 10.1016/j.celrep.2017.06.011

[…] for control, ta, tbx16, and ta;tbx16 double morphants at 75% epiboly (8 hpf; ) were downloaded from geo: gse12857, cyclic loess normalized, and differential expression determined using the r package onechannelgui (). data for ndr1 overexpression in blastulae were previously described (; geo: gse51894)., for gsea (, ), gsea v2.2.2 was used applying 2,000 permutations to gene lists preranked […]

PMCID: 5442466
PMID: 28157210
DOI: 10.1038/cdd.2016.132

[…] on affymetrix mouse gene 1.0 genechip arrays (affymetrix, high wycombe, uk). background subtraction and normalization were performed using the robust multichip average (rma) algorithm in the onechannelgui package. statistical analysis was conducted using the limma software bioconductor (http://www.bioconductor.org) and the benjamini and hochberg procedure was used for multiple testing […]

PMCID: 5180413
PMID: 28031751
DOI: 10.1186/s12263-016-0543-1

[…] genechip processed were generated using command console software., three biological replicates were generated for each experimental condition. microarray statistical analysis was performed using onechannelgui r package., raw signal intensities were normalized using gcrma method as background correction, and differentially expressed genes were identified with limma analysis selecting […]

PMCID: 5122694
PMID: 27900352
DOI: 10.1016/j.dib.2016.11.010

[…] files (".cel" files) for each of the treatment conditions (including two independent replicates per treatment condition) were used to perform the microarray analyses using the bioconductor package onechannelgui , in the statistical software environment r. three contrasts (see ) were using the rma method . data filtering was performed at signal feature level by interquantile range (iqr) […]


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oneChannelGUI institution(s)
CBM (Cluster in Biomedicine) S.c.r.l., AREA Science Park, Trieste, Italy; Department of Informatics, University of Torino, Torino, Italy; Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
oneChannelGUI funding source(s)
Supported by an Oncogenomics grant from Italian Association for Cancer Research; the Italian Ministero dell’Universitae della Ricerca; the University of Torino; and the Regione Piemonte: bando regionale sulla ricerca scientifica applicata 2004.

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