LedPred

LedPred is an R/Bioconductor package that uses support vector machines (SVMs) to predict regulatory sequences. It provides a user-friendly interface to preprocess DNA sequences and train SVM models for prediction. LedPred can predict transcription factor binding sites and other cis-regulatory elements using either DNA sequence information alone or a combination of DNA sequence and gene expression data. It also offers visualization tools for interpreting the results. The package is open source and freely available on Bioconductor. LedPred is a useful tool for researchers working in the field of gene regulation and functional genomics.

Topic

Sequencing;Molecular interactions, pathways and networks;Machine learning

Detail

  • Operation: Pathway or network prediction

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: The MIT License + file license

  • Cost: Free

  • Version name: 1.32.0

  • Credit: ANR, partner of the ERASysBio+ supported under the UE ERA-NET Plus scheme in FP7

  • Input: -

  • Output: -

  • Contact: aitor.gonzalez@univ-amu.fr

  • Collection: -

  • Maturity: Stable

Publications

  • LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines.
  • Seyres D, et al. LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines. LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines. 2016; 32:1091-3. doi: 10.1093/bioinformatics/btv705
  • https://doi.org/10.1093/bioinformatics/btv705
  • PMID: 26628586
  • PMC: -

Download and documentation

< Back to DB search