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README.md
<!-- README.md is generated from README.Rmd. Please edit that file --> # 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)](https://doi.org/doi:10.18129/B9.bioc.idpr) ## Installation You can install the stable release version version from [Bioconductor](https://doi.org/doi:10.18129/B9.bioc.idpr) with: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("idpr") ``` You can install the development version from [Bioconductor](https://bioconductor.org/packages/devel/bioc/html/idpr.html) with: ``` r 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](https://github.com/wmm27/idpr) with: ``` r # 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: ``` r 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]] ``` <img src="man/figures/README-example-1.png" width="75%" /> #> #> [[2]] <img src="man/figures/README-example-2.png" width="75%" /> #> #> [[3]] <img src="man/figures/README-example-3.png" width="75%" /> #> #> [[4]] <img src="man/figures/README-example-4.png" width="75%" /> #> #> [[5]] <img src="man/figures/README-example-5.png" width="75%" /> #> #> [[6]] <img src="man/figures/README-example-6.png" width="75%" /> **Please Refer to idpr-vignette.Rmd file for a detailed introduction to the** **idpr package.** [Link to the Vignette (here)](https://bioconductor.org/packages/release/bioc/vignettes/idpr/inst/doc/idpr-vignette.html) ## Appendix ### Package citation ``` r 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 1.6.1. #> #> 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 1.6.1}, #> } ``` ### Additional Information ``` r Sys.time() #> [1] "2022-03-11 02:31:26 EST" Sys.Date() #> [1] "2022-03-11" R.version #> _ #> platform x86_64-apple-darwin17.0 #> arch x86_64 #> os darwin17.0 #> system x86_64, darwin17.0 #> status #> major 4 #> minor 1.3 #> year 2022 #> month 03 #> day 10 #> svn rev 81868 #> language R #> version.string R version 4.1.3 (2022-03-10) #> nickname One Push-Up ```