QDNAseq protocols

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description
QDNAseq computational protocol

QDNAseq specifications

Information


Unique identifier OMICS_05902
Name QDNAseq
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 1.16.0
Stability Stable
Requirements
methods, stats, graphics, utils, R(>=3.1.0), Biobase(>=2.18.0), CGHbase(>=1.18.0), CGHcall(>=2.18.0), DNAcopy(>=1.32.0), GenomicRanges(>=1.20), IRanges(>=2.2), matrixStats(>=0.50.2), R.utils(>=2.3.0), Rsamtools(>=1.20), BiocParallel(>=1.6.6), BiocStyle(>=1.8.0), BSgenome(>=1.38.0), digest(>=0.6.8), GenomeInfoDb(>=1.6.0), future(>=0.14.0), R.cache(>=0.12.0)
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Daoud Sie <>

Publication for QDNAseq

QDNAseq IN pipeline

2017
PMCID: 5514073
PMID: 28717136
DOI: 10.1038/s41598-017-05623-3

[…] 2.2.4) ‘markduplicates’ feature and these were excluded from downstream analysis along with reads of low mapping quality and supplementary alignments., cna calling was performed in r43 using the qdnaseq pipeline44. briefly, sequence reads were allocated into equally sized (here 1 mb and 50 kb) non-overlapping bins throughout the length of the genome. read counts in each bin were corrected […]

QDNAseq institution(s)
Department of Pathology, VU University Medical Center, Amsterdam, Netherlands

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