Bayesian Model Optimized Reference Correction Method for Assigned and Unassigned Protein NMR Spectra

Provides reference correction for protein NMR spectra. Bayesian Model Optimized Reference Correction (BaMORC) is utilizing Bayesian probabilistic framework to perform protein NMR referencing correction, currently for alpha and beta carbon-13 chemical shifts, without any resonance assignment and/or three-dimensional protein structure. For more detailed explanation, please refer to the paper "Automatic 13C Chemical Shift Reference Correction for Unassigned Protein NMR Spectra" < https://rdcu.be/4ly5> (Journal of Biomolecular NMR, Aug 2018)" .


Build Status CRAN

The BaMORC package is designed to facilitate protein NMR research with an easy-to-use tool that detects and corrects 13C referencing errors before and after the protein resonance assignment step.

Key features:

  • Functions for calculating referencing correction value for assigned and unassigned carbon protein NMR spectra: bamorc() and unassigned_bamorc().

  • Functions for data processing:

    • read_raw_file(), processing user-provided data file.
    • read_nmrstar_file(), automatically process BMRB Star 2.0 and 3.0 files.
    • read_db_file(), automatically fetch BMRB data and output appropriate format via BMRB entry ID number.
  • JPred secondary structure estimation wrapper: jpred_fetcher().

  • CLI functions for using shell.

BaMORC wouldn't be possible without the hard work of the authors of RBMRB and jpredapir. Thanks!

Installation

The latest stable version can be installed from CRAN:

install.packages('BaMORC')

The latest development version can be installed from github:

# install.packages("devtools")
devtools::install_github('https://github.com/MoseleyBioinformaticsLab/BaMORC')

Installing unassigned BaMORC dependencies:

To use unassigned protein NMR reference correction method, SSC (Variance informed DBSCAN for protein NMR spin system clustering.) docker image is required and user need to install docker and SSC docker image

  • Install Docker from here.

  • Install SSC docker image after docker is installed by running following code:

docker pull moseleybioinformaticslab/ssc .

Package usage:

For detailed usage tutorial please refer to Quick Start

CLI usage:

To use "BaMORC CLI", you need to find the CLI run-script. Open terminal and type the following code:

You will see the R script location print out in the terminal as shown in following image.

And to test the R CLI script using the following pattern.

> <path to the R ClI scirpt>/bamorc.R -h

In my example code, it should be like:

> /Users/bill/Library/R/3.5/library/BaMORC/exec/bamorc.R -h

For detailed documation please refere to CLI guide

News

BaMORC 1.0.1

Minor change

Update the VignetteIndexEntry.

BaMORC 1.0

Major changes

  • initial preparation for CRAN submission on CRAN 2018-10-18.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("BaMORC")

1.0.1 by Xi Chen, 4 months ago


https://github.com/MoseleyBioinformaticsLab/BaMORC


Report a bug at https://github.com/MoseleyBioinformaticsLab/BaMORC/issues


Browse source code at https://github.com/cran/BaMORC


Authors: Xi Chen [aut, cre] , Andrey Smelter [aut] , Hunter Moseley [aut]


Documentation:   PDF Manual  


BSD_3_clause + file LICENSE license


Imports data.table, tidyr, DEoptim, httr, docopt, stringr, jsonlite, readr, devtools, RBMRB, BMRBr

Suggests knitr, rmarkdown, formatR


See at CRAN