TDCor: Gene Network Inference from Time-Series Transcriptomic Data
Version 0.1-2

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.

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AuthorJulien Lavenus
Date of publication2015-10-26 15:58:36
MaintainerMikael Lucas <mikael.lucas@ird.fr>
LicenseGPL (>= 2)
Version0.1-2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("TDCor")

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

Functions

CalculateDPI Man page Source code
CalculateTPI Man page Source code
LR_dataset Man page
TDCOR Man page Source code
TDCor-package Man page
TF Man page
UpdateDPI Man page Source code
UpdateTPI Man page Source code
clean.at Man page Source code
cor.data Source code
cor.delay Source code
df_TDCOR Source code
diamonds.filter Source code
directness.index Source code
dpi.bs Source code
dpi.index Source code
draw.profile Man page Source code
entry.points Source code
estimate.delay Man page Source code
estimate.delay.cor Source code
estimate.multi.delay.cor Source code
intersect Source code
isr.index Source code
l_genes Man page
l_names Man page
l_prior Man page
local.max Source code
local.min Source code
make.groups Source code
min.element Source code
minto0 Source code
minto0maxto1 Source code
norm.data Source code
overlap.index Source code
prediction_L_norm Source code
prediction_doubleL_norm Source code
prediction_multiL_ff_norm Source code
shortest.path Man page Source code
ssq.delay Source code
substract Source code
table.nw Source code
times Man page
to.bool Source code
tpi.bs Source code
tpi.index Source code
triangles.filter Source code

Files

NAMESPACE
data
data/l_genes.rda
data/times.rda
data/l_prior.rda
data/LR_dataset.rda
data/l_names.rda
data/TF.rda
R
R/norm.data.R
R/TDCOR.R
R/substract.R
R/CalculateDPI.R
R/UpdateDPI.R
R/entry.points.R
R/prediction_doubleL_norm.R
R/shortest.path.R
R/local.max.R
R/isr.index.R
R/local.min.R
R/estimate.delay.cor.R
R/triangles.filter.R
R/make.groups.R
R/minto0.R
R/diamonds.filter.R
R/CalculateTPI.R
R/overlap.index.R
R/ssq.delay.R
R/clean.at.R
R/dpi.index.R
R/to.bool.R
R/UpdateTPI.R
R/min.element.R
R/cor.delay.R
R/df_TDCOR.R
R/table.nw.R
R/draw.profile.R
R/directness.index.R
R/tpi.bs.R
R/dpi.bs.R
R/tpi.index.R
R/minto0maxto1.R
R/cor.data.R
R/estimate.multi.delay.cor.R
R/prediction_multiL_ff_norm.R
R/intersect.R
R/prediction_L_norm.R
R/estimate.delay.R
MD5
DESCRIPTION
man
man/l_prior.Rd
man/times.Rd
man/TF.Rd
man/l_names.Rd
man/draw.profile.Rd
man/LR_dataset.Rd
man/TDCor-package.Rd
man/clean.at.Rd
man/TDCOR.Rd
man/UpdateDPI.Rd
man/UpdateTPI.Rd
man/CalculateDPI.Rd
man/l_genes.Rd
man/estimate.delay.Rd
man/shortest.path.Rd
man/CalculateTPI.Rd
TDCor documentation built on May 20, 2017, 5:14 a.m.