TEQC statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TEQC
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Tool usage distribution map

This map represents all the scientific publications referring to TEQC per scientific context
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TEQC specifications

Information


Unique identifier OMICS_03602
Name TEQC
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 4.2.0
Stability Stable
Requirements
methods, Rsamtools, BiocGenerics(>=0.1.0), hwriter, Biobase(>=2.15.1), IRanges(>=1.13.5)
Maintained Yes

Versioning


No version available

Documentation


Publication for TEQC

TEQC citations

 (4)
library_books

UroMark—a urinary biomarker assay for the detection of bladder cancer

2017
Clin Epigenetics
PMCID: 5282868
PMID: 28163793
DOI: 10.1186/s13148-016-0303-5

[…] GRCh37) using Bismark v0.7.12 []. Methylation information was extracted using the methylation extractor tool of Bismark v0.7.12 []. Targeted DNA sequencing analyses were performed using the R package TEQC v3.2.0 []. […]

library_books

Low Input Whole Exome Sequencing to Determine the Representation of the Tumor Exome in Circulating DNA of Non Small Cell Lung Cancer Patients

2016
PLoS One
PMCID: 4987014
PMID: 27529345
DOI: 10.1371/journal.pone.0161012

[…] ion-based exome sequencing. In order to evaluate the exome enrichment performance, we estimated the percentage of reads aligned to the target as well as the target region coverage using the R package TEQC []. A fraction of 84% of the uniquely and properly paired cfDNA reads were mapped to the target region, resulting in a median exome sequencing depth of 68.5x (range 38x to 85x, ). No differences […]

library_books

Assessment of RainDrop BS seq as a method for large scale, targeted bisulfite sequencing

2014
Epigenetics
PMCID: 4063826
PMID: 24518816
DOI: 10.4161/epi.28041

[…] information was extracted using the methylation_extractor tool of Bismark v0.7.12 (parameters: -p, -comprehensive, -merge_non_CpG). Targeted DNA sequencing analyses were performed using the R package TEQC v3.2.0. All statistical analyses were performed in R, an environment for statistical computing. […]

library_books

Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture

2013
Leukemia
PMCID: 3768109
PMID: 23702683
DOI: 10.1038/leu.2013.117

[…] Coverage histograms and tables describing the coverage distribution for our set of targeted bases were produced using TEQC, ‘Target Enrichment Quality Control' Bioconductor package. To validate the ability of our assay to identify copy number changes, we used read numbers of two X-linked genes (HPRT and KDM6A). First […]


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TEQC institution(s)
Core Facilities, Centre for Genomic Regulation, UPF, Barcelona, Spain

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