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

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TDCor.pdf |TDCor.html✨
TDCor/json (API)

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

On CRAN:

Conda-Forge:

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 169 downloads 1 mentions 9 exports 1 dependencies

Last updated 9 years agofrom:56cb383764. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 11 2025
R-4.5-winOKFeb 11 2025
R-4.5-macOKFeb 11 2025
R-4.5-linuxOKFeb 11 2025
R-4.4-winOKFeb 11 2025
R-4.4-macOKFeb 11 2025
R-4.3-winOKFeb 11 2025
R-4.3-macOKFeb 11 2025

Exports:CalculateDPICalculateTPIclean.atdraw.profileestimate.delayshortest.pathTDCORUpdateDPIUpdateTPI

Dependencies:deSolve