QDNAseq protocols

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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 r using the qdnaseq pipeline. 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 […]


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QDNAseq in publications

 (15)
PMCID: 5719346
PMID: 29215049
DOI: 10.1038/s41598-017-17525-5

[…] and a high-output nextseq. 500 flow-cell (illumina, san diego, usa)., cnv data analysis was performed as described by deleye et al. using the vivar software. the cnv calls were detected based on the qdnaseq algorithm. the results were analyzed using 1 mb windows. the cnv profiles are visualized as line plots in which the windows are represented as dots, ordered based on their genomic position, […]

PMCID: 5640240
PMID: 29028833
DOI: 10.1371/journal.ppat.1006668

[…] decreased cell viability and increased gene copy number in crispr/cas9 screens [], copy numbers of every 50-kb segment of mkl-1 genome were called from the input of chip-seq experiments using qdnaseq software. segmented copy numbers were converted to copy numbers per gene based on gene coordinates. mageck-vispr pipeline was used to assess data quality, correct copy number variation effect […]

PMCID: 5685714
PMID: 29163793
DOI: 10.18632/oncotarget.21163

[…] coverage analyses were performed using torrent suite version 5.0.2 (ion torrent, carlsbad, ca). genome-wide copy number alterations were first called from aligned, non-pcr-duplicate reads using the qdnaseq r package (version 1.6.1) []. segmented copy-number events were identified using bin-level corrected, median- and control-normalized read counts using the circular binary segmentation […]

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 r using the qdnaseq pipeline. 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 […]

PMCID: 5500342
PMID: 28683077
DOI: 10.1371/journal.pone.0180467

[…] the dna amount did not allow further experimental comparisons. to determine if wgs gc bias could lead to erroneous copy number calls, even after appropriate corrections, we analysed all data using qdnaseq [] in 100 kb bins (). there were possible losses, but with minimally negative logr, in the sc cerebellar sample, which were absent in puregene. these would probably be dismissed as noise, […]


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

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