Package: topdownr 1.29.0

Sebastian Gibb

topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.

Authors:Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard Jensen [aut]

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topdownr.pdf |topdownr.html✨
topdownr/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/sgibb/topdownr/issues

Datasets:
  • tds - TopDownSet Example Data

On BioConductor:topdownr-1.29.0(bioc 3.21)topdownr-1.28.0(bioc 3.20)

immunooncologyinfrastructureproteomicsmassspectrometrycoveragemass-spectrometrytopdown

5.26 score 1 stars 220 downloads 33 exports 128 dependencies

Last updated 23 days agofrom:9e53e8cbe7. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:aggregateassayDatabestConditionscolDatacolData<-combineconditionDataconditionData<-conditionNamescreateExperimentsFragmentOptimisationcreateTngFusionMethFilesexpandMs1ConditionsexpandTms2ConditionsfilterCvfilterInjectionTimefilterIntensityfilterNonReplicatedFragmentsfragmentationMapFragmentViewsmznormalizereadTopDownFilesremoveEmptyConditionsrowViewsrunScanHeadsmanrunXmlMethodChangershowsummaryupdateConditionNamesupdateMedianInjectionTimevalidMs1SettingsvalidTms2SettingswriteMethodXmls

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelBiostringsbslibcachemcliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCorepromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxfunXMLXVectoryamlzlibbioc

Data Generation for topdownr

Pavel V. Shliaha, Sebastian Gibb, Ole Nørregaard Jensen

Rendered fromdata-generation.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2018-12-07
Started: 2017-08-01

Fragmentation Analysis with topdownr

Pavel V. Shliaha, Sebastian Gibb, Ole Nørregaard Jensen

Rendered fromanalysis.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2019-11-22
Started: 2017-08-01

Readme and manuals

Help Manual

Help pageTopics
Investigation of Fragmentation Conditions in Top-Down Proteomicstopdownr-package topdownr
The AbstractTopDownSet class$,AbstractTopDownSet-method $<-,AbstractTopDownSet-method AbstractTopDownSet-class assayData,AbstractTopDownSet-method colData colData,AbstractTopDownSet-method colData<- colData<-,AbstractTopDownSet-method combine combine,AbstractTopDownSet,AbstractTopDownSet-method conditionData conditionData,AbstractTopDownSet-method conditionData<- conditionData<-,AbstractTopDownSet-method conditionNames conditionNames,AbstractTopDownSet-method dim,AbstractTopDownSet-method dimnames,AbstractTopDownSet-method removeEmptyConditions removeEmptyConditions,AbstractTopDownSet-method rowViews rowViews,AbstractTopDownSet-method show,AbstractTopDownSet-method summary,AbstractTopDownSet-method updateConditionNames updateConditionNames,AbstractTopDownSet-method updateMedianInjectionTime updateMedianInjectionTime,AbstractTopDownSet-method updateMedianInjectionTime,TopDownSet-method [,AbstractTopDownSet,ANY,ANY,ANY-method [[,AbstractTopDownSet,ANY,missing,-method [[,AbstractTopDownSet,ANY,missing-method [[<-,AbstractTopDownSet,ANY,missing,-method [[<-,AbstractTopDownSet,ANY,missing-method
Create fragment optimisation experimentcreateExperimentsFragmentOptimisation
Windows specific functions.createTngFusionMethFiles runScanHeadsman runXmlMethodChanger
Expand MS ConditionsexpandMs1Conditions expandTms2Conditions
The FragmentViews classcoerce,FragmentViews,data.frame-method combine,FragmentViews,FragmentViews-method combine,FragmentViews-method FragmentViews FragmentViews-class mz,FragmentViews-method show,FragmentViews-method
The NCBSet classbestConditions bestConditions,NCBSet-method fragmentationMap fragmentationMap,NCBSet-method NCBSet-class show,NCBSet-method summary,NCBSet-method
Read top-down files.readTopDownFiles
TopDownSet Example Datatds
Deprecated functions in topdownrtopdownr-deprecated
The TopDownSet classaggregate,TopDownSet-method coerce,TopDownSet,MSnSet-method coerce,TopDownSet,NCBSet-method combine,TopDownSet,TopDownSet-method filterCv filterCv,TopDownSet-method filterInjectionTime filterInjectionTime,TopDownSet-method filterIntensity filterIntensity,TopDownSet-method filterNonReplicatedFragments filterNonReplicatedFragments,TopDownSet-method normalize,TopDownSet-method plot,TopDownSet,missing-method show,TopDownSet-method summary,TopDownSet-method TopDownSet-class
List valid MS settings.validMs1Settings validTms2Settings
Create Orbitrap Fusion Lumos method.xml files.writeMethodXmls