CRAN/E | BMRBr

BMRBr

'BMRB' File Downloader

Installation

About

Nuclear magnetic resonance (NMR) is a highly versatile analytical technique for studying molecular configuration, conformation, and dynamics, especially those of biomacromolecules such as proteins. Biological Magnetic Resonance Data Bank ('BMRB') is a repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules. Currently, 'BMRB' offers an R package 'RBMRB' to fetch data, however, it doesn't easily offer individual data file downloading and storing in a local directory. When using 'RBMRB', the data will stored as an R object, which fundamentally hinders the NMR researches to access the rich information from raw data, for example, the metadata. Here, 'BMRBr' File Downloader ('BMRBr') offers a more fundamental, low level downloader, which will download original deposited .str format file. This type of file contains information such as entry title, authors, citation, protein sequences, and so on. Many factors affect NMR experiment outputs, such as temperature, resonance sensitivity and etc., approximately 40% of the entries in the 'BMRB' have chemical shift accuracy problems [1,2] Unfortunately, current reference correction methods are heavily dependent on the availability of assigned protein chemical shifts or protein structure. This is my current research project is going to solve, which will be included in the future release of the package. The current version of the package is sufficient and robust enough for downloading individual 'BMRB' data file from the 'BMRB' database . The functionalities of this package includes but not limited: * To simplifies NMR researches by combine data downloading and results analysis together. * To allows NMR data reaches a broader audience that could utilize more than just chemical shifts but also metadata. * To offer reference corrected data for entries without assignment or structure information (future release). Reference: [1] E.L. Ulrich, H. Akutsu, J.F. Doreleijers, Y. Harano, Y.E. Ioannidis, J. Lin, et al., BioMagResBank, Nucl. Acids Res. 36 (2008) D402–8. doi:10.1093/nar/gkm957. [2] L. Wang, H.R. Eghbalnia, A. Bahrami, J.L. Markley, Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications, J. Biomol. NMR. 32 (2005) 13–22. doi:10.1007/s10858-005-1717-0.

github.com/billchenxi/BMRBr
Bug report File report

Key Metrics

Version 0.2.0
R ≥ 3.1.0
Published 2018-08-24 2061 days ago
Needs compilation? no
License GPL-3
CRAN checks BMRBr results

Downloads

Yesterday 2
Last 7 days 88 -40%
Last 30 days 490 +1%
Last 90 days 1.644 +42%
Last 365 days 5.353 +12%

Maintainer

Maintainer

Xi Chen

billchenxi@gmail.com

Authors

Xi Chen

aut / cre

Material

README
NEWS
Reference manual
Package source

Vignettes

BMRBr Package

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

BMRBr archive

Depends

R ≥ 3.1.0
xml2
rvest
utils

Suggests

knitr
rmarkdown
testthat