The Time-Delay Correlation algorithm (TDCor) reconstructs 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 developed to infer the topology of the GRN controlling lateral root formation in Arabidopsis thaliana. The time-series transcriptomic dataset which was used in this study is included in the package to illustrate how to use it.

Author | Julien Lavenus |

Date of publication | 2015-10-26 15:58:36 |

Maintainer | Mikael Lucas <mikael.lucas@ird.fr> |

License | GPL (>= 2) |

Version | 0.1-2 |

**CalculateDPI:** Generate the DPI database to be used by the TDCOR main...

**CalculateTPI:** Generate the TPI database to be used by the TDCOR main...

**clean.at:** Elimininate from a vector of gene codes the genes for which...

**draw.profile:** Plot the expression profile of a 'gene' in 'dataset'

**estimate.delay:** Estimate the time shift between two gene profiles and make a...

**l_genes:** l_genes

**l_names:** l_names

**l_prior:** l_prior

**LR_dataset:** Lateral root transcriptomic dataset

**shortest.path:** Calculate the shortest path linking every pairs of nodes in...

**TDCOR:** The TDCOR main function

**TDCor-package:** TDCor algorithm for gene regulatory network inference

**TF:** Table of 1834 Arabidopsis Transcription factors

**times:** The 'times' vector to use with the lateral root dataset

**UpdateDPI:** Update or check the DPI database

**UpdateTPI:** Update or check the TPI database

TDCor

TDCor/NAMESPACE

TDCor/data

TDCor/data/l_genes.rda

TDCor/data/times.rda

TDCor/data/l_prior.rda

TDCor/data/LR_dataset.rda

TDCor/data/l_names.rda

TDCor/data/TF.rda

TDCor/R

TDCor/R/norm.data.R
TDCor/R/TDCOR.R
TDCor/R/substract.R
TDCor/R/CalculateDPI.R
TDCor/R/UpdateDPI.R
TDCor/R/entry.points.R
TDCor/R/prediction_doubleL_norm.R
TDCor/R/shortest.path.R
TDCor/R/local.max.R
TDCor/R/isr.index.R
TDCor/R/local.min.R
TDCor/R/estimate.delay.cor.R
TDCor/R/triangles.filter.R
TDCor/R/make.groups.R
TDCor/R/minto0.R
TDCor/R/diamonds.filter.R
TDCor/R/CalculateTPI.R
TDCor/R/overlap.index.R
TDCor/R/ssq.delay.R
TDCor/R/clean.at.R
TDCor/R/dpi.index.R
TDCor/R/to.bool.R
TDCor/R/UpdateTPI.R
TDCor/R/min.element.R
TDCor/R/cor.delay.R
TDCor/R/df_TDCOR.R
TDCor/R/table.nw.R
TDCor/R/draw.profile.R
TDCor/R/directness.index.R
TDCor/R/tpi.bs.R
TDCor/R/dpi.bs.R
TDCor/R/tpi.index.R
TDCor/R/minto0maxto1.R
TDCor/R/cor.data.R
TDCor/R/estimate.multi.delay.cor.R
TDCor/R/prediction_multiL_ff_norm.R
TDCor/R/intersect.R
TDCor/R/prediction_L_norm.R
TDCor/R/estimate.delay.R
TDCor/MD5

TDCor/DESCRIPTION

TDCor/man

TDCor/man/l_prior.Rd
TDCor/man/times.Rd
TDCor/man/TF.Rd
TDCor/man/l_names.Rd
TDCor/man/draw.profile.Rd
TDCor/man/LR_dataset.Rd
TDCor/man/TDCor-package.Rd
TDCor/man/clean.at.Rd
TDCor/man/TDCOR.Rd
TDCor/man/UpdateDPI.Rd
TDCor/man/UpdateTPI.Rd
TDCor/man/CalculateDPI.Rd
TDCor/man/l_genes.Rd
TDCor/man/estimate.delay.Rd
TDCor/man/shortest.path.Rd
TDCor/man/CalculateTPI.Rd
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