Package: topdownr 1.35.0

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]

topdownr_1.35.0.tar.gz
topdownr_1.35.0.zip(r-4.7)topdownr_1.35.0.zip(r-4.6)topdownr_1.35.0.zip(r-4.5)
topdownr_1.35.0.tgz(r-4.6-any)topdownr_1.35.0.tgz(r-4.5-any)
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topdownr_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
topdownr/json (API)

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

Bug tracker:https://codeberg.org/sgibb/topdownr

Datasets:
  • tds - TopDownSet Example Data

On BioConductor:topdownr-1.35.0(bioc 3.24)topdownr-1.34.0(bioc 3.23)

immunooncologyinfrastructureproteomicsmassspectrometrycoverage

4.70 score 33 exports 128 dependencies

Last updated from:b3262a2923. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING258
linux-devel-x86_64NOTE820
source / vignettesOK339
linux-release-x86_64NOTE503
macos-release-arm64NOTE253
macos-oldrel-arm64NOTE223
windows-develNOTE442
windows-releaseNOTE404
windows-oldrelNOTE499
wasm-releaseOK209

Exports:aggregateassayDatabestConditionscolDatacolData<-combineconditionDataconditionData<-conditionNamescreateExperimentsFragmentOptimisationcreateTngFusionMethFilesexpandMs1ConditionsexpandTms2ConditionsfilterCvfilterInjectionTimefilterIntensityfilterNonReplicatedFragmentsfragmentationMapFragmentViewsmznormalizereadTopDownFilesremoveEmptyConditionsrowViewsrunScanHeadsmanrunXmlMethodChangershowsummaryupdateConditionNamesupdateMedianInjectionTimevalidMs1SettingsvalidTms2SettingswriteMethodXmls

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelBiostringsbslibcachemcliclueclustercodetoolscpp11crayoncrosstalkcurldata.tableDelayedArraydigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMSnbaseMultiAssayExperimentmzIDmzRncdf4opensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCorepromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxfunXMLXVectoryaml

Fragmentation Analysis with topdownr
Foreword | Questions and bugs | Introduction/Working with topdownr | Importing Files | The TopDownSet Anatomy | Technical Details | Fragment data | Condition data | Assay data | Subsetting a TopDownSet | Plotting a TopDownSet | Fragmentation Data Analysis of Myoglobin | Filter Conditions on Injection Times | Filter Fragments on CV | Filter Fragments on Intensity | Data Aggregation | Random Forest | Combining Fragmentation Conditions to Maximize Coverage | Building a Fragmentation Map | Session Information | References
Rendered fromanalysis.Rmdusingknitr::rmarkdown

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

Data Generation for topdownr
Foreword | Questions and bugs | Introduction | The topdownr Data Generation Workflow | Installation of Additional Software | Setup the Thermo Software | Setup XMLMethodChanger | Setup Operating System | Setup ScanHeadsman | Creating Methods | Data preparation with topdownr | Data Acquisition | Data Preparation | Extracting Header Information | Convert .raw files into mzML | Session Info | References
Rendered fromdata-generation.Rmdusingknitr::rmarkdown

Last update: 2018-12-07
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