draw.profile plots the expression profile of gene in dataset with respect to times.
● Data Source:
CranContrib
● Keywords: Side functions
● Alias: draw.profile
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TDCor (Time-Delay Correlation) is an algorithm designed to infer the topology of a gene regulatory network (GRN) from time-series transcriptomic data. The algorithm is described in details in Lavenus et al., Plant Cell, 2015. It was initially developped to infer the topology of the GRN controlling lateral root formation in Arabidopsis thaliana. The time-series transcriptomic dataset analysed in this study is included in the package.
● Data Source:
CranContrib
● Keywords:
● Alias: TDCor-package
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clean.at removes from a vector of gene codes l_genes all the elements for which no data is present in the matrix dataset.
● Data Source:
CranContrib
● Keywords: Side functions
● Alias: clean.at
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This is the main function to run the TDCOR algorithm and reconstruct the gene network topology.
● Data Source:
CranContrib
● Keywords: Main functions
● Alias: TDCOR
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UpdateDPI analyzes the DPI database and add new entries into it if it does not contain all the necessary data for reconstructing the network with the genes listed in the vector l_genes.
● Data Source:
CranContrib
● Keywords: Main functions
● Alias: UpdateDPI
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UpdateTPI analyzes the TPI database and add new entries into it if it does not contain all the necessary data for reconstructing the network with the genes listed in the vector l_genes.
● Data Source:
CranContrib
● Keywords: Main functions
● Alias: UpdateTPI
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CalculateDPI
(Package: TDCor) :
Generate the DPI database to be used by the TDCOR main function
CalculateDPI builds a DPI database for the TDCOR main function to prune diamond motifs
● Data Source:
CranContrib
● Keywords: Main functions
● Alias: CalculateDPI
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estimate.delay computes the delay/time shift between two gene expression profiles contained in dataset. It returns a list with one or two estimated time shifts and their associated correlation. By default the function also returns a plot composed of four panels which show in more details how these estimate were obtained. This can help the user finding the appropriate parameter values to be used with the TDCOR main function. For more details see below.
● Data Source:
CranContrib
● Keywords: Side functions
● Alias: estimate.delay
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shortest.path computes the shortest influence path (in number of edges) linking every possible regulator/target pairs in the network.
● Data Source:
CranContrib
● Keywords: Side functions
● Alias: shortest.path
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CalculateTPI
(Package: TDCor) :
Generate the TPI database to be used by the TDCOR main function
CalculateTPI builds a TPI database for the TDCOR main function to prune triangle motifs
● Data Source:
CranContrib
● Keywords: Main functions
● Alias: CalculateTPI
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providing 
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