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affy2sv specifications

Information


Unique identifier OMICS_08639
Name affy2sv
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format .CEL files
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Python, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Juan R. González <>

Publication for affy2sv

affy2sv citations

 (3)
library_books

Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type specific vulnerabilities

2018
PMCID: 5905129
PMID: 29692895
DOI: 10.1186/s40170-018-0177-4

[…] contamination 0.02. annovar [] was used to annotate variants., dna libraries were hybridized onto affymetrix cytoscanhd arrays. we first processed the raw intensity cel files using the r package affy2sv [] to generate b-allele frequency (baf) and log r ratio (lrr) values. secondly, we used the penncnv software (parameters: exome hmm model with gcmodel adjustment, filtered by 10 snps minimum […]

library_books

Integrated Analysis of Copy Number Variations and Gene Expression Profiling in Hepatocellular carcinoma

2017
PMCID: 5585301
PMID: 28874807
DOI: 10.1038/s41598-017-11029-y

[…] data (in cel format) of affy snp 6.0 array, in addition to spotting the sites of snps. second, r package of pd.genomewidesnp.6 was used to obtain the annotations of sites of each snp spotted. third, affy2sv package along with penncnv software helped to obtain all information regarding cnvs. according to the genetic annotations obtained, we completed the awk procedure and got the genetic […]

library_books

Identification of miRNA and genes involving in osteosarcoma by comprehensive analysis of microRNA and copy number variation data

2017
PMCID: 5652194
PMID: 29098032
DOI: 10.3892/ol.2017.6845

[…] was performed using the gplots package v3.0.1 (https://cran.r-project.org/web/packages/gplots/index.html)., for gse33153, the log r ratio (lrr) and b allele frequency (baf) were extracted using the affy2sv package v1.0.12 (https://bitbucket.org/brge/affy2sv), and then cnv calling was performed using penncnv v2014 (07) (http://penncnv.openbioinformatics.org/). cnv identified in ≥4 samples […]


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affy2sv institution(s)
Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
affy2sv funding source(s)
This work was partly supported by the Spanish Ministry of Science and Innovation (MTM2011-26515), FIS PI1002512 and a predoctoral fellowship of the Universitat Pompeu Fabra.

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