README.md

In idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

idpr

Overall, ‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins within R. This package is used to identify known characteristics of IDPs within a sequence of interest with easily reported and dynamic results. Additionally, this package also includes tools for IDP-based sequence analysis to be used in conjunction with other R packages.

Please Refer to idpr-vignette.Rmd file for a detailed introduction to the idpr package.

Links to the vignettes found at the Bioconductor landing page (here)

Installation

You can install the stable release version version from Bioconductor with:

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

BiocManager::install("idpr")

You can install the development version from Bioconductor with:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

Or you can install the most recent development version from GitHub with:

# install.packages("devtools") #if not already installed
devtools::install_github("wmm27/idpr")

Example

This is a basic example to quickly profile your protein of interest:

library(idpr)

P53_HUMAN <- TP53Sequences[2] #Getting a pre-loaded sequence from idpr
print(P53_HUMAN)
#>                                                                                                                                                                                                                                                                                                                                                                                            P04637|P53_HUMAN 
#> "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD"

P53_ID <- "P04637" #Human TP53 UniProt ID

idprofile(sequence = P53_HUMAN, #Generates the Profile
          uniprotAccession = P53_ID)
#> [[1]]

#> 
#> [[2]]

#> 
#> [[3]]

#> 
#> [[4]]

#> 
#> [[5]]

Please Refer to idpr-vignette.Rmd file for a detailed introduction to the idpr package. Link to the Vignette (here)

Appendix

Package citation

citation("idpr")
#> 
#> To cite package 'idpr' in publications use:
#> 
#>   William M. McFadden and Judith L. Yanowitz (2020). idpr: Profiling
#>   and Analyzing Intrinsically Disordered Proteins in R. R package
#>   version 1.0.005.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R},
#>     author = {William M. McFadden and Judith L. Yanowitz},
#>     year = {2020},
#>     note = {R package version 1.0.005},
#>   }

Additional Information

Sys.time()
#> [1] "2020-12-23 14:07:28 EST"
Sys.Date()
#> [1] "2020-12-23"
R.version
#>                _                           
#> platform       x86_64-apple-darwin17.0     
#> arch           x86_64                      
#> os             darwin17.0                  
#> system         x86_64, darwin17.0          
#> status                                     
#> major          4                           
#> minor          0.3                         
#> year           2020                        
#> month          10                          
#> day            10                          
#> svn rev        79318                       
#> language       R                           
#> version.string R version 4.0.3 (2020-10-10)
#> nickname       Bunny-Wunnies Freak Out

idpr documentation built on Dec. 26, 2020, 6 p.m.