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TAPS specifications

Information


Unique identifier OMICS_02571
Name TAPS
Alternative name Tumor Aberration Prediction Suite
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Tumor Aberration Prediction Suite

TAPS citations

 (5)
library_books

Investigation of Acute Flaccid Paralysis Reported with La Crosse Virus Infection, Ohio, USA, 2008–2014

2017
PMCID: 5708243
PMID: 29148398
DOI: 10.3201/eid2312.170944

[…] tract pathology) (). Upper motor neuron signs included increased muscle tone or spasticity, increased deep-tendon reflexes, the presence of Babinski and Hoffmann signs, abnormally slow finger or toe taps out of proportion to weakness, or a clear upper motor neuron pattern of weakness (e.g., hemiparesis involving the face, arm, and leg). In addition, a brain lesion that corresponded to the patient […]

library_books

Mutation Processes in 293 Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B

2016
PLoS One
PMCID: 4862684
PMID: 27163364
DOI: 10.1371/journal.pone.0155391

[…] Hawthorne, CA), using the matched mother clone as a reference. SNPRank segmentation was applied and the segmented copy number data were further processed with the Tumor Aberrations Prediction Suite (TAPS) to obtain allele-specific copy number profiles []. All analyses were performed using the R statistical environment (http://www.R-project.org). The number of copy number alterations in the A3B-eG […]

call_split

Microsatellite instability and mutations in BRAF and KRAS are significant predictors of disseminated disease in colon cancer

2015
BMC Cancer
PMCID: 4364587
PMID: 25884297
DOI: 10.1186/s12885-015-1144-x
call_split See protocol

[…] ion algorithm [,] with default settings. Genome-wide average DNA copy number (ploidy) and the proportion of the genome with allelic imbalance were determined using Tumour Aberration Prediction Suite (TAPS) []. Average DNA copy number was calculated as the mean copy number of all genomic segments, weighted on segment length. Near diploid tumours were defined to have average copy number <2.5 and ane […]

call_split

1p36 deletion is a marker for tumour dissemination in microsatellite stable stage II III colon cancer

2014
BMC Cancer
PMCID: 4251789
PMID: 25420937
DOI: 10.1186/1471-2407-14-872
call_split See protocol

[…] nk Segmentation algorithm based on Circular Binary Segmentation [] and default settings. Analyses of absolute allele-specific copy numbers, average ploidy and normal cell content were performed using TAPS []. Copy number estimates are included in the Additional file .CNA frequencies (gain to >2 copies per cell, loss to <2 copies per cell, relative gain to >1.25* individual sample average copy numb […]

library_books

HaplotypeCN: Copy Number Haplotype Inference with Hidden Markov Model and Localized Haplotype Clustering

2014
PLoS One
PMCID: 4029584
PMID: 24849202
DOI: 10.1371/journal.pone.0096841

[…] copy number and probe intensity are approximately linearly correlated on a log-log scale.Several recent researches studied allele-specific copy numbers. The studies of Olshen et al ., Chen et al and Tumor Aberration Prediction Suite (TAPS) are among this category. TAPS adopts Circular Binary Segmentation (CBS) to detect the CNV region. It provides allelic imbalance ratio calculation, and copy nu […]

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TAPS institution(s)
Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden

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