chromWaveR: R package to predict nucleosome occupancy from DNA sequence using pre-trained chromWave models.

Abstract

Requirements

• Install following python packages:

  # CPU version 
  pip install tensorflow==2 keras numpy
  # GPU version 
  pip install tensorflow-gpu==2 keras numpy

• ALTERNATIVE: Setup Tensorflow/Keras CONDA env:

  1. Download and install CONDA.

  2. Install python packages

  conda create -n keras python
  # CPU version 
  pip install tensorflow==2 keras numpy
  # GPU version 
  pip install tensorflow-gpu==2 keras numpy

• Install following R packages from CRAN:

  install.packages(c('tidyverse', 'reticulate', 'kerasR'))

• Install following R packages from Bioconductor:

  install.packages(c('tidyverse', 'reticulate', 'kerasR'))

• Install chromWaveR:

  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  
  BiocManager::install("Biostrings")

Tutorial

For an example of how to use the package see here.

Reference

ChromWave: Deciphering the DNA-encoded competition between DNA-binding factors with deep neural networks

Preprint: Add link upon submission.