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BMRBr
View on CRAN: Click
here
Download and install BMRBr package within the R console
Install from CRAN:
install.packages("BMRBr")
Install from Github:
library("remotes")
install_github("cran/BMRBr")
Install by package version:
library("remotes")
install_version("BMRBr", "0.2.0")
Attach the package and use:
library("BMRBr")
Maintained by
Xi Chen
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-01-17
Latest Update: 2018-08-24
Description:
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
How to cite:
Xi Chen (2018). BMRBr: 'BMRB' File Downloader. R package version 0.2.0, https://cran.r-project.org/web/packages/BMRBr
Previous versions and publish date:
0.1.0 (2018-01-17 10:12)
Other packages that cited BMRBr R package
View BMRBr citation profile
Other R packages that BMRBr depends,
imports, suggests or enhances
Functions, R codes and Examples using
the BMRBr R package
Some associated functions: bmrb_download . collect_ids .
Some associated R codes: bmrb_download.R . collect_ids.R . Full BMRBr package functions and examples
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