Package: Rtpca 1.23.0

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_1.23.0.tar.gz
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Rtpca_1.23.0.tgz(r-4.6-any)Rtpca_1.23.0.tgz(r-4.5-any)
Rtpca_1.23.0.tar.gz(r-4.7-any)Rtpca_1.23.0.tar.gz(r-4.6-any)
Rtpca_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rtpca/json (API)

# Install 'Rtpca' in R:

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

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-1.23.0(bioc 3.24)Rtpca-1.22.0(bioc 3.23)

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

software proteomics dataimport

4.68 score 32 scripts 1 mentions 40 exports 34 dependencies

Last updated from:46e133ad9c. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	166
linux-devel-x86_64	NOTE	208
source / vignettes	OK	201
linux-release-x86_64	NOTE	250
macos-release-arm64	NOTE	112
macos-oldrel-arm64	NOTE	137
windows-devel	NOTE	117
windows-release	NOTE	111
windows-oldrel	NOTE	116
wasm-release	OK	161

Exports:CommonFeatures ComplexAnnotation ComplexBackgroundDistributionList ComplexRocTable ContrastCondName ContrastDistMat ContrastList createDistMat CtrlCondName diffTpcaResultTable DistMat DistMethod ObjList plotComplexRoc plotDiffTpcaVolcano plotPPiProfiles plotPPiRoc plotTpcaVolcano PPiAnnotation PPiRocTable PPiRocTableAnno runDiffTPCA runTPCA SetCommonFeatures SetComplexAnnotation SetComplexBackgroundDistributionList SetComplexRocTable SetContrastCondName SetContrastDistMat SetCtrlCondName SetDiffTpcaResultTable SetDistMat SetDistMethod SetPPiRocTable SetPPiRocTableAnno SetSummaryMethod SetTpcaResultTable SummaryMethod tpcaResult tpcaResultTable

Dependencies:Biobase BiocGenerics cli cpp11 dplyr farver fdrtool generics ggplot2 glue gtable isoband labeling lifecycle magrittr pillar pkgconfig pROC purrr R6 RColorBrewer Rcpp rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Introduction to Rtpca

Rendered fromRtpca.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract CommonFeatures	CommonFeatures CommonFeatures,tpcaResult-method
Extract ComplexAnnotation	ComplexAnnotation ComplexAnnotation,tpcaResult-method
Extract ComplexBackgroundDistributionList	ComplexBackgroundDistributionList ComplexBackgroundDistributionList,tpcaResult-method
Extract ComplexRocTable	ComplexRocTable ComplexRocTable,tpcaResult-method
Extract ContrastCondName	ContrastCondName ContrastCondName,tpcaResult-method
Extract ContrastDistMat	ContrastDistMat ContrastDistMat,tpcaResult-method
Extract ContrastList	ContrastList ContrastList,tpcaResult-method
Create distance matrix of all vs all protein melting profiles	createDistMat
Extract CtrlCondName	CtrlCondName CtrlCondName,tpcaResult-method
Extract diffTpcaResultTable	diffTpcaResultTable diffTpcaResultTable,tpcaResult-method
Extract DistMat	DistMat DistMat,tpcaResult-method
Extract DistMethod	DistMethod DistMethod,tpcaResult-method
Extract ObjList	ObjList 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 900	ori_et_al_complex_ppis
Data frame of annotated protein complexes by Ori et al.	ori_et_al_complexes_df
Plot Complex ROC curve	plotComplexRoc
Plot differential TPCA analysis results	plotDiffTpcaVolcano
Plot thermal profile of protein pairs	plotPPiProfiles
Plot PPI ROC curve	plotPPiRoc
Plot TPCA analysis results	plotTpcaVolcano
Extract PPiAnnotation	PPiAnnotation PPiAnnotation,tpcaResult-method
Extract PPiRocTable	PPiRocTable PPiRocTable,tpcaResult-method
Extract PPiRocTableAnno	PPiRocTableAnno PPiRocTableAnno,tpcaResult-method
Run differential TPCA analysis	runDiffTPCA
Run the TPCA analysis	runTPCA
Set CommonFeatures	SetCommonFeatures SetCommonFeatures,tpcaResult-method
Set ComplexAnnotation	SetComplexAnnotation SetComplexAnnotation,tpcaResult-method
Set ComplexBackgroundDistributionList	SetComplexBackgroundDistributionList SetComplexBackgroundDistributionList,tpcaResult-method
Set ComplexRocTable	SetComplexRocTable SetComplexRocTable,tpcaResult-method
Set ContrastCondName	SetContrastCondName SetContrastCondName,tpcaResult-method
Set ContrastDistMat	SetContrastDistMat SetContrastDistMat,tpcaResult-method
Set CtrlCondName	SetCtrlCondName SetCtrlCondName,tpcaResult-method
Set diffTpcaResultTable	SetDiffTpcaResultTable SetDiffTpcaResultTable,tpcaResult-method
Set DistMat	SetDistMat SetDistMat,tpcaResult-method
Set distMethod	SetDistMethod SetDistMethod,tpcaResult-method
Set PPiRocTable	SetPPiRocTable SetPPiRocTable,tpcaResult-method
Set PPiRocTableAnno	SetPPiRocTableAnno SetPPiRocTableAnno,tpcaResult-method
Set summaryMethod	SetSummaryMethod SetSummaryMethod,tpcaResult-method
Set TpcaResultTable	SetTpcaResultTable SetTpcaResultTable,tpcaResult-method
Data frame of annotated human protein-protein interactions retrieved from stringDB with a combined interaction score equal or higher than 700	string_ppi_df
Extract SummaryMethod	SummaryMethod SummaryMethod,tpcaResult-method
S4 TPCA Result Class	tpcaResult tpcaResult-class
Extract tpcaResultTable	tpcaResultTable tpcaResultTable,tpcaResult-method