Package: idpr 1.23.0

William M. McFadden

idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins (IDPs) within R. This package is used to identify known characteristics of IDPs for a sequence of interest with easily reported and dynamic results. Additionally, this package includes tools for IDP-based sequence analysis to be used in conjunction with other R packages. Described in McFadden WM & Yanowitz JL (2022). "idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R." PloS one, 17(4), e0266929. <https://doi.org/10.1371/journal.pone.0266929>.

Authors:William M. McFadden [cre, aut], Judith L. Yanowitz [aut, fnd], Michael Buszczak [ctb, fnd]

idpr_1.23.0.tar.gz
idpr_1.23.0.zip(r-4.7)idpr_1.23.0.zip(r-4.6)idpr_1.23.0.zip(r-4.5)
idpr_1.23.0.tgz(r-4.6-any)idpr_1.23.0.tgz(r-4.5-any)
idpr_1.23.0.tar.gz(r-4.7-any)idpr_1.23.0.tar.gz(r-4.6-any)
idpr_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
idpr/json (API)

# Install 'idpr' in R:
install.packages('idpr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wmm27/idpr/issues

Datasets:
  • Disorder40 - Disorder-based Substitution Matrices.
  • Disorder60 - Disorder-based Substitution Matrices.
  • Disorder85 - Disorder-based Substitution Matrices.
  • DUNMat - A Substitution Matrix for Aligning Intrinsically Disordered Proteins
  • EDSSMat50 - EDSSMat Disorder-based Substitution Matrices.
  • EDSSMat60 - EDSSMat Disorder-based Substitution Matrices.
  • EDSSMat62 - EDSSMat Disorder-based Substitution Matrices.
  • EDSSMat70 - EDSSMat Disorder-based Substitution Matrices.
  • EDSSMat75 - EDSSMat Disorder-based Substitution Matrices.
  • EDSSMat80 - EDSSMat Disorder-based Substitution Matrices.
  • EDSSMat90 - EDSSMat Disorder-based Substitution Matrices.
  • GorillaTP53 - Human Cellular tumor antigen p53 and homologs
  • KDNorm - Kyte and Doolittle Scaled Hydropathy Index
  • pKaData - Sets of pKa values for Charged Amino Acids
  • TP53Sequences - Human Cellular tumor antigen p53 and homologs

On BioConductor:idpr-1.23.0(bioc 3.24)idpr-1.22.0(bioc 3.23)

structuralpredictionproteomicscellbiology

6.26 score 5 stars 30 scripts 395 downloads 19 exports 35 dependencies

Last updated from:a9e232c4d2. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING198
linux-devel-x86_64OK223
source / vignettesOK279
linux-release-x86_64OK258
macos-release-arm64OK112
macos-oldrel-arm64OK99
windows-develOK138
windows-releaseOK156
windows-oldrelOK166
wasm-releaseOK143

Exports:chargeCalculationGlobalchargeCalculationLocalchargeHydropathyPlotfoldIndexRhendersonHasselbalchidprofileiuprediupredAnchoriupredRedoxmeanScaledHydropathynetChargescaledHydropathyGlobalscaledHydropathyLocalsequenceChecksequenceMapsequenceMapCoordinatessequencePlotstructuralTendencystructuralTendencyPlot

Dependencies:BiocGenericsBiostringsclicpp11crayondplyrfarvergenericsggplot2gluegtableIRangesisobandjsonlitelabelinglifecyclemagrittrpillarpkgconfigplyrR6RColorBrewerRcpprlangS4VectorsS7scalesSeqinfotibbletidyselectutf8vctrsviridisLitewithrXVector

Disordered Matrices Vignette
Substitution Matrices for Intrinsically Disordered Proteins | Quick Intro | Installation | Background and Motivation | Matrices | EDSS Matrices | "Disorder" Matrices | DUNMat | Examples | Pairwise Sequence Alignments (PSAs) | Multiple Sequence Alignments (MSAs) | Distance Trees | References | Packages | Citations | Additional Information
Rendered fromdisorderedMatrices-vignette.Rmdusingknitr::rmarkdown

Last update: 2024-04-23
Started: 2020-06-11

Charge and Hydropathy Vignette
Background | Installation | Methods | Example calulations | Using the chargeHydropathyPlot Function | Using FoldIndexR to predict folded and unfolded windows. | Calculating Scaled Hydropathy | Mean Scaled Hydropathy | Global Hydropathy | Local Hydrophobicity | Calculating Charge | Net Charge | Global Charge Distibution | Local Charge | References | Packages Used | Citations | Additional Information
Rendered fromchargeHydropathy-vignette.Rmdusingknitr::rmarkdown

Last update: 2022-12-10
Started: 2020-06-11

idpr Package Overview Vignette
idpr: A Package for Profiling and Analyzing Intrinsically Disordered Proteins in R. | Installation | Profiling | Charge-Hydropathy Plot and FoldIndex | Structural Tendency Plot | Local Charge Calculations | Local Hydropathy | IUPred | Visualizing Discrete Values | Substitution Matrices for Analyzing IDPs | References | Additional Information
Rendered fromidpr-vignette.Rmdusingknitr::rmarkdown

Last update: 2022-12-10
Started: 2020-06-11

IUPred Vignette
Fetching IUPred Predictions of Intrinsic Disorder | Quick Start | Background | Installation | iupred function and iupredType arguments. | iupredType = "long" | iupredType = "short" | iupredType = "glob" | iupredAnchor | iupredRedox | Additional Example | Getting the UniProt Accession | Use | References | Additional Information
Rendered fromiupred-vignette.Rmdusingknitr::rmarkdown

Last update: 2022-12-10
Started: 2020-06-11

Sequence Map Vignette
Introduction | Installation | Basics of sequenceMap | Customizations | Getting Coordinates | Sequence Plot | References | Packages Used | Citations | Additional Information
Rendered fromsequenceMAP-vignette.Rmdusingknitr::rmarkdown

Last update: 2022-12-10
Started: 2020-06-11

Structural Tendency Vignette
Background | Installation | Quick-use guide | structuralTendency In Detail | structuralTendencyPlot In Detail | References | Citations | Additional Information
Rendered fromstructuralTendency-vignette.Rmdusingknitr::rmarkdown

Last update: 2022-12-10
Started: 2020-06-11