Package: Rtpca 1.17.0

Nils Kurzawa

Rtpca: Thermal proximity co-aggregation with R

R package for performing thermal proximity co-aggregation analysis with thermal proteome profiling datasets to analyse protein complex assembly and (differential) protein-protein interactions across conditions.

Authors:Nils Kurzawa [aut, cre], André Mateus [aut], Mikhail M. Savitski [aut]

Rtpca_1.17.0.tar.gz
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Rtpca.pdf |Rtpca.html✨
Rtpca/json (API)
NEWS

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

Peer review:

Datasets:
  • ori_et_al_complex_ppis - Data frame of eukaryotic protein-protein interactions inferred from annotated protein complexes by Ori et al. and StringDB interations with a combined score of at least 900
  • ori_et_al_complexes_df - Data frame of annotated protein complexes by Ori et al.
  • string_ppi_df - Data frame of annotated human protein-protein interactions retrieved from stringDB with a combined interaction score equal or higher than 700

On BioConductor:Rtpca-1.17.0(bioc 3.21)Rtpca-1.16.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwareproteomicsdataimport

4.46 score 29 scripts 190 downloads 1 mentions 39 exports 42 dependencies

Last updated 2 months agofrom:28c7a1056c. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winNOTENov 30 2024
R-4.5-linuxNOTENov 30 2024
R-4.4-winNOTENov 30 2024
R-4.4-macNOTENov 30 2024
R-4.3-winNOTENov 30 2024
R-4.3-macNOTENov 30 2024

Exports:CommonFeaturesComplexAnnotationComplexBackgroundDistributionListComplexRocTableContrastCondNameContrastDistMatContrastListcreateDistMatCtrlCondNamediffTpcaResultTableDistMatDistMethodObjListplotComplexRocplotDiffTpcaVolcanoplotPPiProfilesplotPPiRocplotTpcaVolcanoPPiAnnotationPPiRocTablePPiRocTableAnnorunDiffTPCArunTPCASetCommonFeaturesSetComplexAnnotationSetComplexBackgroundDistributionListSetComplexRocTableSetContrastCondNameSetContrastDistMatSetCtrlCondNameSetDiffTpcaResultTableSetDistMatSetDistMethodSetPPiRocTableSetPPiRocTableAnnoSetSummaryMethodSetTpcaResultTableSummaryMethodtpcaResultTable

Dependencies:BiobaseBiocGenericsclicolorspacecpp11dplyrfansifarverfdrtoolgenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrpROCpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Introduction to Rtpca

Nils Kurzawa

Rendered fromRtpca.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2020-11-27
Started: 2019-12-13

Readme and manuals

Help Manual

Help pageTopics
Extract CommonFeaturesCommonFeatures CommonFeatures,tpcaResult-method
Extract ComplexAnnotationComplexAnnotation ComplexAnnotation,tpcaResult-method
Extract ComplexBackgroundDistributionListComplexBackgroundDistributionList ComplexBackgroundDistributionList,tpcaResult-method
Extract ComplexRocTableComplexRocTable ComplexRocTable,tpcaResult-method
Extract ContrastCondNameContrastCondName ContrastCondName,tpcaResult-method
Extract ContrastDistMatContrastDistMat ContrastDistMat,tpcaResult-method
Extract ContrastListContrastList ContrastList,tpcaResult-method
Create distance matrix of all vs all protein melting profilescreateDistMat
Extract CtrlCondNameCtrlCondName CtrlCondName,tpcaResult-method
Extract diffTpcaResultTablediffTpcaResultTable diffTpcaResultTable,tpcaResult-method
Extract DistMatDistMat DistMat,tpcaResult-method
Extract DistMethodDistMethod DistMethod,tpcaResult-method
Extract ObjListObjList ObjList,tpcaResult-method
Data frame of eukaryotic protein-protein interactions inferred from annotated protein complexes by Ori et al. and StringDB interations with a combined score of at least 900ori_et_al_complex_ppis
Data frame of annotated protein complexes by Ori et al.ori_et_al_complexes_df
Plot Complex ROC curveplotComplexRoc
Plot differential TPCA analysis resultsplotDiffTpcaVolcano
Plot thermal profile of protein pairsplotPPiProfiles
Plot PPI ROC curveplotPPiRoc
Plot TPCA analysis resultsplotTpcaVolcano
Extract PPiAnnotationPPiAnnotation PPiAnnotation,tpcaResult-method
Extract PPiRocTablePPiRocTable PPiRocTable,tpcaResult-method
Extract PPiRocTableAnnoPPiRocTableAnno PPiRocTableAnno,tpcaResult-method
Run differential TPCA analysisrunDiffTPCA
Run the TPCA analysisrunTPCA
Set CommonFeaturesSetCommonFeatures SetCommonFeatures,tpcaResult-method
Set ComplexAnnotationSetComplexAnnotation SetComplexAnnotation,tpcaResult-method
Set ComplexBackgroundDistributionListSetComplexBackgroundDistributionList SetComplexBackgroundDistributionList,tpcaResult-method
Set ComplexRocTableSetComplexRocTable SetComplexRocTable,tpcaResult-method
Set ContrastCondNameSetContrastCondName SetContrastCondName,tpcaResult-method
Set ContrastDistMatSetContrastDistMat SetContrastDistMat,tpcaResult-method
Set CtrlCondNameSetCtrlCondName SetCtrlCondName,tpcaResult-method
Set diffTpcaResultTableSetDiffTpcaResultTable SetDiffTpcaResultTable,tpcaResult-method
Set DistMatSetDistMat SetDistMat,tpcaResult-method
Set distMethodSetDistMethod SetDistMethod,tpcaResult-method
Set PPiRocTableSetPPiRocTable SetPPiRocTable,tpcaResult-method
Set PPiRocTableAnnoSetPPiRocTableAnno SetPPiRocTableAnno,tpcaResult-method
Set summaryMethodSetSummaryMethod SetSummaryMethod,tpcaResult-method
Set TpcaResultTableSetTpcaResultTable SetTpcaResultTable,tpcaResult-method
Data frame of annotated human protein-protein interactions retrieved from stringDB with a combined interaction score equal or higher than 700string_ppi_df
Extract SummaryMethodSummaryMethod SummaryMethod,tpcaResult-method
S4 TPCA Result ClasstpcaResult tpcaResult-class
Extract tpcaResultTabletpcaResultTable tpcaResultTable,tpcaResult-method