Package: TPP2D 1.23.0

Nils Kurzawa

TPP2D: Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)

Detection of ligand-protein interactions from 2D thermal profiles (DLPTP), Performs an FDR-controlled analysis of 2D-TPP experiments by functional analysis of dose-response curves across temperatures.

Authors:Nils Kurzawa [aut, cre], Holger Franken [aut], Simon Anders [aut], Wolfgang Huber [aut], Mikhail M. Savitski [aut]

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TPP2D.pdf |TPP2D.html✨
TPP2D/json (API)
NEWS

# Install 'TPP2D' in R:
install.packages('TPP2D', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • config_tab - Example config table for a import of a simulated 2D-TPP cell extract dataset
  • raw_dat_list - Example raw data for a subset of a simulated 2D-TPP cell extract dataset
  • simulated_cell_extract_df - Example subset of a simulated 2D-TPP cell extract dataset

On BioConductor:TPP2D-1.23.0(bioc 3.21)TPP2D-1.22.0(bioc 3.20)

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

softwareproteomicsdataimport

4.20 score 16 scripts 149 downloads 30 exports 54 dependencies

Last updated 2 months agofrom:9179fb5309. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 22 2024
R-4.5-winNOTEDec 22 2024
R-4.5-linuxNOTEDec 22 2024
R-4.4-winNOTEDec 22 2024
R-4.4-macNOTEDec 22 2024
R-4.3-winNOTEDec 22 2024
R-4.3-macNOTEDec 22 2024

Exports:annotateDataListbootstrapNullbootstrapNullAlternativeModelbootstrapNullAlternativeModelFastcompeteModelscomputeFstatcomputeFStatFromParamsconfigWide2LongfilterOutContaminantsfindHitsfitAndEvalDatasetfitH0ModelfitH1ModelgetFDRgetModelParamsDfgetPEC504TemperaturegetPvaluesgg_qqimport2dDatasetimport2dMainplot2dTppFcHeatmapplot2dTppFitplot2dTppProfileplot2dTppRelProfileplot2dTppVolcanorecomputeSignalFromRatiosrenameColumnsresolveAmbiguousProteinNamesrunTPP2DTPP_importCheckConfigTable

Dependencies:BHBiocParallelbitopsclicodetoolscolorspacecpp11doParalleldplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsggplot2gluegtableisobanditeratorslabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixmgcvmunsellnlmeopenxlsxpillarpkgconfigpurrrR6RColorBrewerRcppRCurlrlangscalessnowstatmodstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithrzip

Introduction to TPP2D for 2D-TPP analysis

Nils Kurzawa

Rendered fromTPP2D.Rmdusingknitr::rmarkdownon Dec 22 2024.

Last update: 2022-11-17
Started: 2019-04-15

Readme and manuals

Help Manual

Help pageTopics
Annotate imported data list using a config tableannotateDataList
Bootstrap null distribution of F statistics for FDR estimationbootstrapNull
Bootstrap null distribution of F statistics for FDR estimation based on resampling alternative model residualsbootstrapNullAlternativeModel
Bootstrap null distribution of F statistics for FDR estimation based on resampling alternative model residuals with only one round of model fitting on resampled data and subsequent resampling of thereby obtained residualsbootstrapNullAlternativeModelFast
Compete H0 and H1 models per protein and obtain F statisticcompeteModels
Compute F statistic from H1 and H0 model characteristicscomputeFstat
Compute F statistics from paramter data framecomputeFStatFromParams
Example config table for a import of a simulated 2D-TPP cell extract datasetconfig_tab
Tranform configuration table from wide to longconfigWide2Long
Filter out contaminantsfilterOutContaminants
Find hits according to FDR thresholdfindHits
Fit H0 and H1 model to 2D thermal profiles of proteins and compute F statisticfitAndEvalDataset
Fit H0 model and evaluate fit statisticsfitH0Model
Fit H1 model and evaluate fit statisticsfitH1Model
Get FDR for given F statistics based on true and null datasetgetFDR
Get H0 and H1 model parametersgetModelParamsDf
Get pEC50 for a protein of interest at a specific temperatures (optimally the melting point of the protein)getPEC504Temperature
Compute p-values for given F statistics based on true and null datasetgetPvalues
Plot qq-plot of true data and bootstrapped null with ggplotgg_qq
Import 2D-TPP dataset using a config tableimport2dDataset
Import 2D-TPP dataset main functionimport2dMain
Plot heatmap of 2D thermal profile fold changes of a protein of choiceplot2dTppFcHeatmap
Plot H0 or H1 fit of 2D thermal profile intensities of a protein of choiceplot2dTppFit
Plot 2D thermal profile intensities of a protein of choiceplot2dTppProfile
Plot 2D thermal profile ratios of a protein of choiceplot2dTppRelProfile
Plot Volcano plot of TPP2D resultsplot2dTppVolcano
Example raw data for a subset of a simulated 2D-TPP cell extract datasetraw_dat_list
Recompute robust signal intensities based on bootstrapped TMT channel ratiosrecomputeSignalFromRatios
Rename columns of imported data framerenameColumns
Resolve ambiguous protein namesresolveAmbiguousProteinNames
Run complete TPP2D analysisrunTPP2D
Example subset of a simulated 2D-TPP cell extract datasetsimulated_cell_extract_df
Import and chech configuration tableTPP_importCheckConfigTable
S4 TPP2D Experiment ClasstpcaResult tpp2dExperiment-class