Package: TPP2D 1.29.0

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]

TPP2D_1.29.0.tar.gz
TPP2D_1.29.0.zip(r-4.7)TPP2D_1.29.0.zip(r-4.6)TPP2D_1.29.0.zip(r-4.5)
TPP2D_1.29.0.tgz(r-4.6-any)TPP2D_1.29.0.tgz(r-4.5-any)
TPP2D_1.29.0.tar.gz(r-4.7-any)TPP2D_1.29.0.tar.gz(r-4.6-any)
TPP2D_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TPP2D/json (API)

# Install 'TPP2D' in R:

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

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-1.29.0(bioc 3.24)TPP2D-1.28.0(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

4.41 score 17 scripts 31 exports 48 dependencies

Last updated from:975a781e2a. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	188
linux-devel-x86_64	NOTE	237
source / vignettes	OK	278
linux-release-x86_64	NOTE	237
macos-release-arm64	NOTE	192
macos-oldrel-arm64	NOTE	110
windows-devel	NOTE	174
windows-release	NOTE	165
windows-oldrel	NOTE	151
wasm-release	OK	158

Exports:annotateDataList bootstrapNull bootstrapNullAlternativeModel bootstrapNullAlternativeModelFast competeModels computeFstat computeFStatFromParams configWide2Long filterOutContaminants findHits fitAndEvalDataset fitH0Model fitH1Model getFDR getModelParamsDf getPEC504Temperature getPvalues gg_qq import2dDataset import2dMain plot2dTppFcHeatmap plot2dTppFit plot2dTppProfile plot2dTppRelProfile plot2dTppVolcano recomputeSignalFromRatios renameColumns resolveAmbiguousProteinNames runTPP2D tpcaResult TPP_importCheckConfigTable

Dependencies:BH BiocParallel bitops cli codetools cpp11 doParallel dplyr farver foreach formatR futile.logger futile.options generics ggplot2 glue gtable isoband iterators labeling lambda.r lifecycle limma magrittr MASS openxlsx pillar pkgconfig purrr R6 RColorBrewer Rcpp RCurl rlang S7 scales snow statmod stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr zip

Introduction to TPP2D for 2D-TPP analysis

Rendered fromTPP2D.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate imported data list using a config table	annotateDataList
Bootstrap null distribution of F statistics for FDR estimation	bootstrapNull
Bootstrap null distribution of F statistics for FDR estimation based on resampling alternative model residuals	bootstrapNullAlternativeModel
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 residuals	bootstrapNullAlternativeModelFast
Compete H0 and H1 models per protein and obtain F statistic	competeModels
Compute F statistic from H1 and H0 model characteristics	computeFstat
Compute F statistics from paramter data frame	computeFStatFromParams
Example config table for a import of a simulated 2D-TPP cell extract dataset	config_tab
Tranform configuration table from wide to long	configWide2Long
Filter out contaminants	filterOutContaminants
Find hits according to FDR threshold	findHits
Fit H0 and H1 model to 2D thermal profiles of proteins and compute F statistic	fitAndEvalDataset
Fit H0 model and evaluate fit statistics	fitH0Model
Fit H1 model and evaluate fit statistics	fitH1Model
Get FDR for given F statistics based on true and null dataset	getFDR
Get H0 and H1 model parameters	getModelParamsDf
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 dataset	getPvalues
Plot qq-plot of true data and bootstrapped null with ggplot	gg_qq
Import 2D-TPP dataset using a config table	import2dDataset
Import 2D-TPP dataset main function	import2dMain
Plot heatmap of 2D thermal profile fold changes of a protein of choice	plot2dTppFcHeatmap
Plot H0 or H1 fit of 2D thermal profile intensities of a protein of choice	plot2dTppFit
Plot 2D thermal profile intensities of a protein of choice	plot2dTppProfile
Plot 2D thermal profile ratios of a protein of choice	plot2dTppRelProfile
Plot Volcano plot of TPP2D results	plot2dTppVolcano
Example raw data for a subset of a simulated 2D-TPP cell extract dataset	raw_dat_list
Recompute robust signal intensities based on bootstrapped TMT channel ratios	recomputeSignalFromRatios
Rename columns of imported data frame	renameColumns
Resolve ambiguous protein names	resolveAmbiguousProteinNames
Run complete TPP2D analysis	runTPP2D
Example subset of a simulated 2D-TPP cell extract dataset	simulated_cell_extract_df
Import and chech configuration table	TPP_importCheckConfigTable
S4 TPP2D Experiment Class	tpcaResult tpp2dExperiment-class