Package: TPP 3.35.0

Dorothee Childs

TPP: Analyze thermal proteome profiling (TPP) experiments

Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).

Authors:Dorothee Childs, Nils Kurzawa, Holger Franken, Carola Doce, Mikhail Savitski and Wolfgang Huber

TPP_3.35.0.tar.gz
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TPP.pdf |TPP.html✨
TPP/json (API)
NEWS

# Install 'TPP' in R:

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

Datasets:

hdacCCR_config - The configuration table to analyze hdacCCR_data.
hdacCCR_data - TPP-CCR example dataset
hdacTR_config - The configuration table to analyze hdacTR_data.
hdacTR_data - TPP-TR example dataset.
panobinostat_2DTPP_config - The configuration table to analyze panobinostat_2DTPP_data.
panobinostat_2DTPP_data - 2D-TPP-CCR example dataset
resultTable - Example of a TPP-TR result table.
tppRefData - Example of a reference dataset for 2D-TPP experiments.

On BioConductor:TPP-3.35.0(bioc 3.21)TPP-3.34.0(bioc 3.20)

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

immunooncology proteomics massspectrometry

4.98 score 16 scripts 270 downloads 57 mentions 45 exports 86 dependencies

Last updated 2 months agofrom:d3e2611141. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 30 2024
R-4.5-win	NOTE	Nov 30 2024
R-4.5-linux	NOTE	Nov 30 2024
R-4.4-win	NOTE	Nov 30 2024
R-4.4-mac	NOTE	Nov 30 2024
R-4.3-win	NOTE	Nov 30 2024
R-4.3-mac	NOTE	Nov 30 2024

Exports:analyze2DTPP analyzeTPPCCR analyzeTPPTR tpp2dAddAdditionalInfo tpp2dCalcFractAbundance tpp2dComputeFoldChanges tpp2dCreateCCRConfigFile tpp2dCreateDRplots tpp2dCreateReport tpp2dCreateTPPTRreference tpp2dCurveFit tpp2dEvalConfigTable tpp2dExport tpp2dExportPlots tpp2dImport tpp2dMerge2dRef tpp2dNormalize tpp2dPlotCCRAllCurves tpp2dPlotCCRGoodCurves tpp2dPlotCCRSingleCurves tpp2dPlotQChist tpp2dPlotQCpEC50 tpp2dRemoveZeroSias tpp2dSplineFitAndTest tpp2dTRReferenceObject tppccrCurveFit tppccrImport tppccrNormalize tppccrNormalizeToReference tppccrPlotCurves tppccrResultTable tppccrTransform tppDefaultTheme tppExport tppQCPlotsCorrelateExperiments tpptrAnalyzeMeltingCurves tpptrCurveFit tpptrDefaultNormReqs tpptrFitSplines tpptrFTest tpptrImport tpptrNormalize tpptrPlotSplines tpptrSplineFitAndTest tpptrTidyUpESets

Dependencies:backports base64enc Biobase biobroom BiocGenerics bitops broom bslib cachem cli codetools colorspace cpp11 data.table digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics ggplot2 glue gridExtra gtable highr htmltools isoband iterators jquerylib jsonlite knitr labeling lambda.r lattice lifecycle limma magrittr MASS Matrix mefa memoise mgcv mime munsell nlme nls2 openxlsx pillar pkgconfig plyr proto purrr R6 rappdirs RColorBrewer Rcpp RCurl reshape2 rlang rmarkdown sass scales statmod stringi stringr tibble tidyr tidyselect tinytex utf8 vctrs VennDiagram VGAM viridisLite withr xfun yaml zip

TPP_introduction_1D

Rendered fromTPP_introduction_1D.Rnwusingknitr::knitron Nov 30 2024.

Last update: 2018-08-07
Started: 2016-10-06

TPP_introduction_2D

Rendered fromTPP_introduction_2D.Rnwusingknitr::knitron Nov 30 2024.

Last update: 2021-10-17
Started: 2016-10-06

TPP_introduction_NPARC

Rendered fromNPARC_analysis_of_TPP_TR_data.Rnwusingknitr::knitron Nov 30 2024.

Last update: 2019-10-12
Started: 2016-10-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analyze a 2D-TPP experiment	analyze2DTPP
Analyze TPP-CCR experiment	analyzeTPPCCR
Analyze TPP-TR experiment	analyzeTPPTR
The configuration table to analyze hdacCCR_data.	hdacCCR_config
TPP-CCR example dataset (replicates 1 and 2)	hdacCCR_data
Example subsets of a Panobinostat TPP-CCR dataset (replicates 1 and 2) and the corresponding configuration table to start the analysis.	hdacCCR_smallExample
The configuration table to analyze hdacTR_data.	hdacTR_config
TPP-TR example dataset.	hdacTR_data
Example of a TPP-TR result table.	hdacTR_resultsTable_smallExample
Example subset of a Panobinostat TPP-TR dataset and the corresponding configuration table to start the analysis.	hdacTR_smallExample
The configuration table to analyze panobinostat_2DTPP_data.	panobinostat_2DTPP_config
2D-TPP-CCR example dataset	panobinostat_2DTPP_data
Example subsets of a Panobinostat 2D-TPP dataset and the corresponding configuration table to start the analysis.	panobinostat_2DTPP_smallExample
Example of a TPP-TR result table.	resultTable
Thermal proteome profiling (TPP)	.onLoad TPP
Defunct functions in package 'TPP'	TPP-defunct tpp2dCreateCCRConfigFile tpp2dEvalConfigTable tpp2dPlotCCRAllCurves tpp2dPlotCCRGoodCurves tpp2dPlotCCRSingleCurves tpp2dRemoveZeroSias tpp2dReplaceColNames
Deprecated functions in package 'TPP'	TPP-deprecated
Add additional info to 2D-TPP CCR output data	tpp2dAddAdditionalInfo
Calculate fractional abundance and DMSO ratio of successive sumionareas (usage of function is only reasonable when at least two temperatures are multiplexed!)	tpp2dCalcFractAbundance
Compute 2D-TPP fold changes	tpp2dComputeFoldChanges
Create dose response curve plots for 2D-TPP data	tpp2dCreateDRplots
Create Report of 2D-TPP analysis	tpp2dCreateReport
Create TPP-TR reference for 2D-TPP experiment	tpp2dCreateTPPTRreference
Run TPP-CCR analysis for 2D-TPP experiment	tpp2dCurveFit
Produce Excel table of 2D-TPP experiment.	tpp2dExport
Export plots for 2D-TPP experiment.	tpp2dExportPlots
Import 2D-TPP data	tpp2dImport
Merge 2D-TPP result data with TPP-TR reference data	tpp2dMerge2dRef
Median normalization of protein fold changes of 2D-TPP data	tpp2dNormalize
Plot quality control histograms	tpp2dPlotQChist
Plot quality control pEC50 plots	tpp2dPlotQCpEC50
Fit splines and perform f-Test	tpp2dSplineFitAndTest
Fit splines and generate ggplot visualizations	tpp2dSplinePlot
TPP-TR reference object	tpp2dTRReferenceObject
Fit dose response curves	tppccrCurveFit
Import TPP-CCR dataset for analysis by the 'TPP' package.	tppccrImport
Normalize data from TPP-CCR experiments	tppccrNormalize
Normalize fold changes of TPP-CCR experiment to a reference column	tppccrNormalizeToReference
Plot dose response curves	tppccrPlotCurves
Summarize results of a TPP-CCR study	tppccrResultTable
Transform fold changes of TPP-CCR experiment	tppccrTransform
Default ggplot theme for melting curve plots.	tppDefaultTheme
Produce Excel table of TPP-TR or TPP-CCR experiment.	tppExport
Visually compare fold changes of different TPP experiments.	tppQCPlotsCorrelateExperiments
Example of a reference dataset for 2D-TPP experiments.	tppRefData
Example of a reference dataset for 2D-TPP experiments.	TPPTR_reference_results_HepG2
Analyze fitted curve parameters to detect significant shifts in melting points.	tpptrAnalyzeMeltingCurves
Fit melting curves to all proteins in a dataset.	tpptrCurveFit
Default filter criteria for fold change normalization	tpptrDefaultNormReqs
Perform spline fitting	tpptrFitSplines
Analyze spline fits to detect differential behavior over time	tpptrFTest
Import TPP-TR datasets for analysis by the 'TPP' package.	tpptrImport
Normalize protein fold changes	tpptrNormalize
Plot spline fits per protein	tpptrPlotSplines
Perform spline fitting and analyze by moderated F-test	tpptrSplineFitAndTest
Tidy up expressionSets	tpptrTidyUpESets