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Protocols

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


No version available

Documentation


Maintainer


  • person_outline Daoud Sie <>

Publication for QDNAseq

QDNAseq citations

 (15)
library_books

STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods

2017
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, […]

library_books

Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis

2017
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 […]

library_books

Rapid, ultra low coverage copy number profiling of cell free DNA as a precision oncology screening strategy

2017
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 […]

library_books

Association Of Plasma And Urinary Mutant DNA With Clinical Outcomes In Muscle Invasive Bladder Cancer

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 […]

library_books

DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation

2017
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, […]

library_books

Hi C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours

2017
PMCID: 5488307
PMID: 28655341
DOI: 10.1186/s13059-017-1253-8

[…] we treated it in a manner similar to shallow whole-genome sequencing (swgs), though with some modifications to the hi-c data, and processed both sets of data through the same copy number pipeline (qdnaseq). qdnaseq provides copy number information from dna samples without the requirement for a reference and includes steps to correct for issues caused by mappability and gc content and also […]


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

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