TDCor: Gene Network Inference from Time-Series Transcriptomic Data

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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

View on CRAN

Man pages

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

Files in this package

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