Package: TDCor 0.1-2

TDCor: Gene Network Inference from Time-Series Transcriptomic Data

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.

Authors:Julien Lavenus

TDCor_0.1-2.tar.gz
TDCor_0.1-2.zip(r-4.7)TDCor_0.1-2.zip(r-4.6)TDCor_0.1-2.zip(r-4.5)
TDCor_0.1-2.tgz(r-4.6-any)TDCor_0.1-2.tgz(r-4.5-any)
TDCor_0.1-2.tar.gz(r-4.7-any)TDCor_0.1-2.tar.gz(r-4.6-any)
TDCor_0.1-2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TDCor/json (API)

# Install 'TDCor' in R:
install.packages('TDCor', repos = c('https://lucasmikael.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • l_genes - L_genes
  • l_names - L_names
  • l_prior - L_prior
  • LR_dataset - Lateral root transcriptomic dataset
  • TF - Table of 1834 Arabidopsis Transcription factors
  • times - The 'times' vector to use with the lateral root dataset

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.30 score 20 scripts 129 downloads 1 mentions 9 exports 1 dependencies

Last updated from:56cb383764. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK92
source / vignettesOK158
linux-release-x86_64OK112
macos-release-arm64OK172
macos-oldrel-arm64OK157
windows-develOK69
windows-releaseOK73
windows-oldrelOK77
wasm-releaseOK88

Exports:CalculateDPICalculateTPIclean.atdraw.profileestimate.delayshortest.pathTDCORUpdateDPIUpdateTPI

Dependencies:deSolve