oneChannelGUI statistics

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Citations per year

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

This map represents all the scientific publications referring to oneChannelGUI per scientific context
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Protocols

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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Versioning


No version available

Documentation


Maintainer


  • person_outline Raffaele A. Calogero

Publication for oneChannelGUI

oneChannelGUI citations

 (19)
library_books

Expression of TDRD9 in a subset of lung carcinomas by CpG island hypomethylation protects from DNA damage

2017
Oncotarget
PMCID: 5839389
PMID: 29515758
DOI: 10.18632/oncotarget.22709

[…] lized 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 transcr […]

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In Vivo Regulation of the Zebrafish Endoderm Progenitor Niche by T Box Transcription Factors

2017
Cell Rep
PMCID: 5494305
PMID: 28658625
DOI: 10.1016/j.celrep.2017.06.011
call_split See protocol

[…] 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 on stati […]

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Modulation of macrophage antitumor potential by apoptotic lymphoma cells

2017
Cell Death Differ
PMCID: 5442466
PMID: 28157210
DOI: 10.1038/cdd.2016.132
call_split See protocol

[…] dization 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 cor […]

library_books

Transcriptome Analysis on Monocytes from Patients with Neovascular Age Related Macular Degeneration

2016
Sci Rep
PMCID: 4931446
PMID: 27374485
DOI: 10.1038/srep29046

[…] R Studio, and Bioconductor (http://www.bioconductor.org), as well as Partek Genomics Suite. We utilized multiple R packages for the purpose of the study including affy, oligo, limma, simpleAffy, and oneChannelGUI (R codes are available upon request from the authors). RMA was used for the normalization method, and after RMA, all values continued in log2 transformation. Quality control based on arr […]

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High Persister Mutants in Mycobacterium tuberculosis

2016
PLoS One
PMCID: 4866775
PMID: 27176494
DOI: 10.1371/journal.pone.0155127
call_split See protocol

[…] outliers. Differences in amplification or labeling tend to cause these outliers. Our study did not show any outliers. Statistical analysis of the data was performed using the Bioconductor program and oneChannelGUI package [] available through the R Project for Statistical Computing (www.r-project.org). Data is presented as log2 fold change. The microarray data have been deposited in NCBI’s Gene Ex […]

library_books

Lack of Neuronal IFN β IFNAR Causes Lewy Body and Parkinson’s Disease like Dementia

2015
Cell
PMCID: 4601085
PMID: 26451483
DOI: 10.1016/j.cell.2015.08.069

[…] intensity values, and normal-distributed data were tested in unpaired two-tailed Student’s t tests, filtering for differential regulation confidence of 95% (p < 0.05). Venn diagrams were created with oneChannelGUI (Bioconductor). Quantile-normalized RMA-treated data selected using a 1.4-fold cutoff were analyzed with Ingenuity Pathway Analysis software.GSEA data heatmaps were generated by extracti […]


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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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