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) format files 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.

AuthorKonstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut]
Date of publication2016-12-13 08:25:53
MaintainerKonstantin A. Blagodatskikh <k.blag@yandex.ru>
LicenseGPL (>= 2)
Version0.9-5
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.

Files in this package

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

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