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ddpcr specifications

Information


Unique identifier OMICS_16513
Name ddpcr
Alternative name droplet digital polymerase chain reaction
Interface Web user interface
Restrictions to use None
Programming languages R
License MIT License
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Jennifer Bryan

Information


Unique identifier OMICS_16513
Name ddpcr
Alternative name droplet digital polymerase chain reaction
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 1.9
Stability Stable
Requirements
stats, graphics, utils, rmarkdown, R(≥3.1.0), gridExtra(≥ 2.0.0), DT(≥0.2), dplyr(≥0.5.0), ggplot2(≥2.2.0), lazyeval(≥0.1.10), magrittr(≥1.5), mixtools(≥1.0.2), plyr(≥ 1.8.1), readr(≥0.1.0), shiny(≥0.11.0), shinyjs(≥0.4.0), ggExtra(≥0.3.0), grid(≥3.2.2), knitr(≥1.7), testthat(≥0.11.0)
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Jennifer Bryan

Publication for droplet digital polymerase chain reaction

ddpcr citations

 (37)
library_books

Systematic analysis of copy number variation associated with congenital diaphragmatic hernia

2018
Proc Natl Acad Sci U S A
PMCID: 5960281
PMID: 29712845
DOI: 10.1073/pnas.1714885115

[…] ients tended to have other malformations or medical problems in addition to CDH. All of these chromosomal abnormalities were confirmed by clinical karyotype, clinical microarray, digital droplet PCR (ddPCR), and/or read depth data from WES.To assess the performance of the customized array, we tested all 6 significantly associated CNVs from , 4 large singleton CNVs from , and 14 other randomly chos […]

library_books

Environmental Controls of Oyster Pathogenic Vibrio spp. in Oregon Estuaries and a Shellfish Hatchery

2018
Appl Environ Microbiol
PMCID: 5930336
PMID: 29475863
DOI: 10.1128/AEM.02156-17

[…] Droplet digital PCR (ddPCR) was used to quantify total Vibrio species 16S rRNA gene copies using a Bio-Rad QX200 system. The ddPCR method produces copy number estimates that agree with quantitative PCR (qPCR)-based method […]

library_books

Population based analysis of ocular Chlamydia trachomatis in trachoma endemic West African communities identifies genomic markers of disease severity

2018
Genome Med
PMCID: 5828069
PMID: 29482619
DOI: 10.1186/s13073-018-0521-x

[…] Conjunctival swabs collected during a cross-sectional population-based trachoma survey on the Bijagós Archipelago yielded 220 ocular Ct infections detected by Ct plasmid-based ddPCR. Of the 220 Ct infections detected, 184 were quantifiable using Ct genome-based ddPCR.We obtained WGS data from 126/220 samples using cell culture (n = 8) or direct sequencing from swabs with Su […]

library_books

Clinical signs of trachoma are prevalent among Solomon Islanders who have no persistent markers of prior infection with Chlamydia trachomatis

2018
Wellcome Open Res
PMCID: 5854984
PMID: 29588922
DOI: 10.21956/wellcomeopenres.14575.r31073

[…] All data analyses were conducted using R 3.2.3 . Pre- and post-MDA proportions were compared using Wilcoxon’s rank sum test. Fleiss’ Kappa scores were calculated using the ‘irr’ package in R. ddPCR tests for current ocular Ct infection were classified into negative and positive populations according to methods described previously . Anti-Pgp3 antibody titre was divided into two populations […]

library_books

Whole genome diversity of inherited chromosomally integrated HHV 6 derived from healthy individuals of diverse geographic origin

2018
Sci Rep
PMCID: 5823862
PMID: 29472617
DOI: 10.1038/s41598-018-21645-x

[…] The LCLs from the sequenced samples were tested for the presence of iciHHV-6. Following the method proposed by Sedlack et al., we performed droplet digital PCR (ddPCR) in order to quantify the absolute number of HHV-6 copies and human genome copy. If the virus was present in an inherited form, we would expect to have a copy of its genome per each cell. The re […]

library_books

A robust internal control for high precision DNA methylation analyses by droplet digital PCR

2018
Clin Epigenetics
PMCID: 5822558
PMID: 29484034
DOI: 10.1186/s13148-018-0456-5

[…] The ddPCR technology allows highly sensitive quantification of nucleic acids and has great potential for analyses of DNA methylation. In the present work, we have developed a robust internal control for m […]

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