RDML: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization for the structure of RDML object and GUI for RDML editing.

Install the latest version of this package by entering the following in R:
install.packages("RDML")
AuthorKonstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut]
Date of publication2017-04-24 14:53:01 UTC
MaintainerKonstantin A. Blagodatskikh <k.blag@yandex.ru>
LicenseGPL (>= 2)
Version0.9-6
https://github.com/kablag/RDML

View on CRAN

Man pages

adpsType: adpsType R6 class.

annotationType: annotationType R6 class.

AsDendrogram-function: 'RDML$AsDendrogram()' wrapper

asdendrogram-method: Represents structure of 'RDML' file as dendrogram

astable-function: 'RDML$AsTable()' wrapper

astable-method: Represents fields of 'RDML' object as 'data.frame'

baseTemperatureType: baseTemperatureType R6 class.

cdnaSynthesisMethodType: cdnaSynthesisMethodType R6 class.

commercialAssayType: commercialAssayType R6 class.

cqDetectionMethodType: cqDetectionMethodType R6 class.

dataCollectionSoftwareType: dataCollectionSoftwareType R6 class.

dataType: dataType R6 class.

documentationType: documentationType R6 class.

dyeType: dyeType R6 class.

enumType: enumType R6 class.

experimenterType: experimenterType R6 class.

experimentType: experimentType R6 class.

GetFData-function: 'RDML$GetFData()' wrapper

getfdata-method: Gets fluorescence data vectors from 'RDML' object

gradientType: gradientType R6 class.

idReferencesType: idReferencesType R6 class.

idType: idType R6 class.

labelFormatType: labelFormatType R6 class.

lidOpenType: lidOpenType R6 class.

loopType: loopType R6 class.

mdpsType: mdpsType R6 class.

measureType: measureType R6 class.

MergeRDMLs: Merges 'RDML' objects

new-method: Creates new instance of 'RDML' class object

nucleotideType: nucleotideType R6 class.

oligoType: oligoType R6 class.

pauseType: pauseType R6 class.

pcrFormatType: pcrFormatType R6 class.

primingMethodType: primingMethodType R6 class.

quantityType: quantityType R6 class.

quantityUnitType: quantityUnitType R6 class.

RDML: R6 class 'RDML' - contains methods to read and overview...

rdmlBaseType: Base R6 class for RDML package.

rdmlEdit: RDML Editor Graphical User Interface

rdmlIdType: rdmlIdType R6 class.

reactIdType: reactIdType R6 class.

reactType: reactType R6 class.

runType: runType R6 class.

sampleType: sampleType R6 class.

sampleTypeType: sampleTypeType R6 class.

sequencesType: sequencesType R6 class.

setfdata-function: 'RDML$SetFData()' wrapper

setfdata-method: Sets fluorescence data vectors to 'RDML' object

stepType: stepType R6 class.

targetType: targetType R6 class.

targetTypeType: targetTypeType R6 class.

temperatureType: temperatureType R6 class.

templateQuantityType: templateQuantityType R6 class.

thermalCyclingConditionsType: thermalCyclingConditionsType R6 class.

xRefType: xRefType R6 class.

Functions

adpsType Man page
annotationType Man page
AsDendrogram Man page
AsTable Man page
baseTemperatureType Man page
cdnaSynthesisMethodType Man page
commercialAssayType Man page
cqDetectionMethodType Man page
dataCollectionSoftwareType Man page
dataType Man page
documentationType Man page
dyeType Man page
enumType Man page
experimenterType Man page
experimentType Man page
GetFData Man page
gradientType Man page
idReferencesType Man page
idType Man page
labelFormatType Man page
lidOpenType Man page
loopType Man page
mdpsType Man page
measureType Man page
MergeRDMLs Man page
new Man page
nucleotideType Man page
oligoType Man page
pauseType Man page
pcrFormatType Man page
primingMethodType Man page
quantityType Man page
quantityUnitType Man page
RDML Man page
RDML.AsDendrogram Man page
RDML.AsTable Man page
rdmlBaseType Man page
rdmlEdit Man page
RDML.GetFData Man page
rdmlIdType Man page
RDML.new Man page
RDML.SetFData Man page
reactIdType Man page
reactType Man page
runType Man page
sampleType Man page
sampleTypeType Man page
sequencesType Man page
SetFData Man page
stepType Man page
targetType Man page
targetTypeType Man page
temperatureType Man page
templateQuantityType Man page
thermalCyclingConditionsType Man page
xRefType Man page

Files

inst
inst/RDMLedit
inst/RDMLedit/ui.R inst/RDMLedit/server.R
inst/RDMLedit/www
inst/RDMLedit/www/css
inst/RDMLedit/www/css/styles.css
inst/RDMLedit/www/js
inst/RDMLedit/www/js/scripts.js
inst/RDMLedit/www/js/single_double_click.js
inst/RDMLedit/www/js/my_shinyjs_scripts.js
inst/RDMLedit/md
inst/RDMLedit/md/help.md
inst/RDMLedit/rdml.extensions.R
inst/extdata
inst/extdata/BioRad_qPCR_melt.rdml
inst/extdata/from_abi7500
inst/extdata/from_abi7500/sce.eds
inst/extdata/stepone_std.rdml
inst/extdata/from_tables
inst/extdata/from_tables/table.xlsx
inst/extdata/from_tables/fdata.csv
inst/extdata/lc96_bACTXY.rdml
inst/doc
inst/doc/CreateRDML.R
inst/doc/CreateRDML.Rmd
inst/doc/CreateRDML.html
inst/doc/RDML.Rmd
inst/doc/RDML.R
inst/doc/RDML.html
NAMESPACE
CHANGELOG
R
R/RDML.types.R R/RDML.GetFData.R R/RDML.Merge.R R/rdmlEdit.R R/RDML.SetFData.R R/RDML.AsTable.R R/functional_wrappers.R R/RDML.AsDendrogram.R R/RDML.init.R R/RDML.R
vignettes
vignettes/RDML_logo.png
vignettes/CreateRDML.Rmd
vignettes/rdml_overview_1_2.png
vignettes/data_view.png
vignettes/File_import.png
vignettes/RDML.Rmd
vignettes/RDML.bib
vignettes/bench_df.csv
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/reactType.Rd man/rdmlBaseType.Rd man/experimenterType.Rd man/pcrFormatType.Rd man/lidOpenType.Rd man/adpsType.Rd man/sampleTypeType.Rd man/MergeRDMLs.Rd man/targetTypeType.Rd man/sequencesType.Rd man/templateQuantityType.Rd man/labelFormatType.Rd man/mdpsType.Rd man/idType.Rd man/stepType.Rd man/temperatureType.Rd man/setfdata-function.Rd man/measureType.Rd man/enumType.Rd man/runType.Rd man/astable-function.Rd man/nucleotideType.Rd man/idReferencesType.Rd man/dataType.Rd man/dataCollectionSoftwareType.Rd man/thermalCyclingConditionsType.Rd man/baseTemperatureType.Rd man/xRefType.Rd man/rdmlEdit.Rd man/dyeType.Rd man/oligoType.Rd man/sampleType.Rd man/commercialAssayType.Rd man/loopType.Rd man/primingMethodType.Rd man/getfdata-method.Rd man/AsDendrogram-function.Rd man/pauseType.Rd man/gradientType.Rd man/new-method.Rd man/cdnaSynthesisMethodType.Rd man/annotationType.Rd man/setfdata-method.Rd man/reactIdType.Rd man/RDML.Rd man/GetFData-function.Rd man/documentationType.Rd man/targetType.Rd man/asdendrogram-method.Rd man/astable-method.Rd man/quantityUnitType.Rd man/rdmlIdType.Rd man/experimentType.Rd man/cqDetectionMethodType.Rd man/quantityType.Rd

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Please suggest features or report bugs with the GitHub issue tracker.

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