Package: RDML 1.3

Konstantin A. Blagodatskikh

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.

Authors:Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut], Andrej-Nikolai Spiess [aut]

RDML_1.3.tar.gz
RDML_1.3.zip(r-4.5)RDML_1.3.zip(r-4.4)RDML_1.3.zip(r-4.3)
RDML_1.3.tgz(r-4.4-any)RDML_1.3.tgz(r-4.3-any)
RDML_1.3.tar.gz(r-4.5-noble)RDML_1.3.tar.gz(r-4.4-noble)
RDML_1.3.tgz(r-4.4-emscripten)RDML_1.3.tgz(r-4.3-emscripten)
RDML.pdf |RDML.html✨
RDML/json (API)

# Install 'RDML' in R:
install.packages('RDML', repos = c('https://pcruniversum.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pcruniversum/rdml/issues

On CRAN:

bioinformaticspcrqpcrrdml

6.26 score 21 stars 1 packages 58 scripts 287 downloads 47 exports 34 dependencies

Last updated 3 months agofrom:a898512fd9. Checks:OK: 5 NOTE: 1 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winERROROct 29 2024
R-4.5-linuxNOTEOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:adpsTypeannotationTypeAsDendrogramAsTablecdnaSynthesisMethodTypecommercialAssayTypecqDetectionMethodTypedataCollectionSoftwareTypedataTypedocumentationTypedyeTypeexperimenterTypeexperimentTypeGetFDatagradientTypeidReferencesTypeidTypelabelFormatTypelidOpenTypeloopTypemdpsTypemeasureTypeMergeRDMLsnucleotideTypeoligoTypepauseTypepcrFormatTypeprimingMethodTypequantityTypequantityUnitTypeRDMLrdmlEditrdmlIdTypereactIdTypereactTyperunTypesampleTypesampleTypeTypesequencesTypeSetFDatastepTypetargetTypetargetTypeTypetemperatureTypetemplateQuantityTypethermalCyclingConditionsTypexRefType

Dependencies:backportscellrangercheckmateclicpp11crayondata.tablefansigenericsgluehmsjsonlitelifecyclelubridatemagrittrpillarpipeRpkgconfigprettyunitsprogressR6readxlrematchrlangrliststringistringrtibbletimechangeutf8vctrsXMLxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Extract data points from 'RDML' object[.GetFData [.RDML
adpsType R6 class.adpsType
annotationType R6 class.annotationType
Convert 'idType' object to 'character'as.character.idType
Convert 'reactIdType' object to 'character'as.character.reactIdType
'RDML$AsDendrogram()' wrapperAsDendrogram
'RDML$AsTable()' wrapperAsTable
baseTemperatureType R6 class.baseTemperatureType
cdnaSynthesisMethodType R6 class.cdnaSynthesisMethodType
commercialAssayType R6 class.commercialAssayType
cqDetectionMethodType R6 class.cqDetectionMethodType
dataCollectionSoftwareType R6 class.dataCollectionSoftwareType
dataType R6 class.dataType
documentationType R6 class.documentationType
dyeType R6 class.dyeType
enumType R6 class.enumType
experimenterType R6 class.experimenterType
experimentType R6 class.experimentType
'RDML$GetFData()' wrapperGetFData
gradientType R6 class.gradientType
idReferencesType R6 class.idReferencesType
idType R6 class.idType
labelFormatType R6 class.labelFormatType
lidOpenType R6 class.lidOpenType
loopType R6 class.loopType
mdpsType R6 class.mdpsType
measureType R6 class.measureType
Merges 'RDML' objectsMergeRDMLs
Creates new instance of 'RDML' class objectnew RDML.new
nucleotideType R6 class.nucleotideType
oligoType R6 class.oligoType
pauseType R6 class.pauseType
pcrFormatType R6 class.pcrFormatType
primingMethodType R6 class.primingMethodType
quantityType R6 class.quantityType
quantityUnitType R6 class.quantityUnitType
R6 class 'RDML' - contains methods to read and overview fluorescence data from RDML v1.1 and v1.2 format filesRDML
Represents structure of 'RDML' file as dendrogramRDML.AsDendrogram
Represents fields of 'RDML' object as 'data.frame'RDML.AsTable
Gets fluorescence data vectors from 'RDML' objectRDML.GetFData
Sets fluorescence data vectors to 'RDML' objectRDML.SetFData
Base R6 class for RDML package.rdmlBaseType
RDML Editor Graphical User InterfacerdmlEdit
rdmlIdType R6 class.rdmlIdType
reactIdType R6 class.reactIdType
reactType R6 class.reactType
runType R6 class.runType
sampleType R6 class.sampleType
sampleTypeType R6 class.sampleTypeType
sequencesType R6 class.sequencesType
'RDML$SetFData()' wrapperSetFData
stepType R6 class.stepType
targetType R6 class.targetType
targetTypeType R6 class.targetTypeType
temperatureType R6 class.temperatureType
templateQuantityType R6 class.templateQuantityType
thermalCyclingConditionsType R6 class.thermalCyclingConditionsType
xRefType R6 class.xRefType