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rCGH specifications

Information


Unique identifier OMICS_10932
Name rCGH
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data As input rCGH supports Agilent Human CGH data, from 44K to 400K, and Affymetrix, SNP6 and cytoScanHD. All are provided in text format by platform-specific software: standard Agilent text files are exported from Agilent Feature Extraction software (FE), while Affymetrix cychp.txt, cnchp.txt or probeset.txt files are obtained by processing Affymetrix CEL files through ChAS or Affymetrix Power Tools (APT) software. Custom arrays can also be supported, provided the data format complies with the requirements.
Output data rCGH stores all the original and computed data, as well as the workflow parameters, to ensure traceability. Segmentation tables are of the same format as standard circular binary segmentation (CBS) outputs, completed with the segment lengths and the within-segment log2 relative ratios (LRR) standard deviation.
Biological technology Affymetrix, Agilent Technologies
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.10.0
Stability Stable
Requirements
AnnotationDbi, limma, methods, stats, plyr, parallel, grid, graphics, BiocGenerics, IRanges, GenomicRanges, DNAcopy, utils, GenomeInfoDb, BiocStyle, grDevices, lattice, ggplot2, affy, RUnit, GenomicFeatures, knitr, aCGH, org.Hs.eg.db, mclust, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, R(>=3.4), shiny(>=0.11.1), TxDb.Hsapiens.UCSC.hg18.knownGene
Maintained Yes

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Publication for rCGH

rCGH in publication

PMCID: 5907722
PMID: 29615097
DOI: 10.1186/s13062-018-0207-8

[…] ile : table s2 was used to select and match the samples for which also microarray and rna-seq data was available. the selected acgh microarray raw data files were preprocessed independently using the rcgh r/bioconductor package [] with default parameters, and segmentation tables were then summarized over genes (“cnv-g”). features with undefined values (na) were removed from all datasets before pro […]


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rCGH institution(s)
INSERM U981, Gustave Roussy, University Paris-Sud, Villejuif, France; Sage Bionetworks, Seattle, WA, USA; Department of Medical Oncology, Gustave Roussy, Villejuif, France
rCGH funding source(s)
This work was supported by the Integrative Cancer Biology Program of the National Cancer Institute (U54CA149237), Unicancer, the ARC foundation, the Breast Cancer Research foundation and Odyssea.

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