项目作者: ruthkr

项目描述 :
An R package to predict RNA structure thermodynamically using sliding windows approach
高级语言: R
项目地址: git://github.com/ruthkr/rnafolding.git
创建时间: 2020-11-26T18:31:37Z
项目社区:https://github.com/ruthkr/rnafolding

开源协议:Other

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rnafolding is a package to…

Installation

You can install the development version from
GitHub with:

  1. # install.packages("devtools")
  2. devtools::install_github("ruthkr/rnafolding")

Quick start

This is a basic example which shows you how to run windowed folding from
a FASTA file:

  1. # Load the package
  2. library(rnafolding)
  3. # Define the FASTA path from the sample 5S rRNA sequence
  4. seq_5S <- system.file("extdata", "5S.fasta", package = "rnafolding")
  5. # Fold 5S with Sliding Windows
  6. windows_5S <- rnafolding::fold(
  7. filename = seq_5S,
  8. winsize = 50,
  9. stepsize = 5
  10. )

After getting the windowed folding results, you can plot the structure
map as follows:

  1. plot_structure_map(
  2. windows_5S,
  3. plot_list = c("entropy", "bpp")
  4. )