Learn R Programming

TPP (version 2.2.3)

Analyze thermal proteome profiling (TPP) experiments

Description

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

Copy Link

Version

Version

2.2.3

License

Artistic-2.0

Maintainer

Dorothee Childs

Last Published

February 15th, 2017

Functions in TPP (2.2.3)

tpptrNormalize

Normalize protein fold changes
analyzeTPPCCR

Analyze TPP-CCR experiment
tppccrTransform

Transform fold changes of TPP-CCR experiment
hdacCCR_config

The configuration table to analyze hdacCCR_data.
TPP

Thermal proteome profiling (TPP)
tpptrCurveFit

Fit melting curves to all proteins in a dataset.
tpptrImport

Import TPP-TR datasets for analysis by the TPP package.
tppccrPlotCurves

Plot dose response curves
hdacTR_data

TPP-TR example dataset.
hdacTR_resultsTable_smallExample

Example of a TPP-TR result table.
resultTable

Example of a TPP-TR result table.
hdacCCR_smallExample

Example subsets of a Panobinostat TPP-CCR dataset (replicates 1 and 2) and the corresponding configuration table to start the analysis.
analyzeTPPTR

Analyze TPP-TR experiment
tppQCPlotsCorrelateExperiments

Visually compare fold changes of different TPP experiments.
tppExport

Produce Excel table of TPP-TR or TPP-CCR experiment.
tppDefaultTheme

Default ggplot theme for melting curve plots.
tpptrDefaultNormReqs

Default filter criteria for fold change normalization
hdacTR_config

The configuration table to analyze hdacTR_data.
tppccrNormalize

Normalize data from TPP-CCR experiments
tppccrResultTable

Summarize results of a TPP-CCR study
hdacCCR_data

TPP-CCR example dataset (replicates 1 and 2)
tppccrCurveFit

Fit dose response curves
tppccrNormalizeToReference

Normalize fold changes of TPP-CCR experiment to a reference column
hdacTR_smallExample

Example subset of a Panobinostat TPP-TR dataset and the corresponding configuration table to start the analysis.
tpptrAnalyzeMeltingCurves

Analyze fitted curve parameters to detect significant shifts in melting points.
tppccrImport

Import TPP-CCR dataset for analysis by the TPP package.