Package: VDAP 2.0.0

Cody Moore

VDAP: Peptide Array Analysis Tools

Analyze Peptide Array Data and characterize peptide sequence space. Allows for high level visualization of global signal, Quality control based on replicate correlation and/or relative Kd, calculation of peptide Length/Charge/Kd parameters, Hits selection based on RFU Signal, and amino acid composition/basic motif recognition with RFU signal weighting. Basic signal trends can be used to generate peptides that follow the observed compositional trends.

Authors:Cody Moore

VDAP_2.0.0.tar.gz
VDAP_2.0.0.tar.gz(r-4.7-any)VDAP_2.0.0.tar.gz(r-4.6-any)
VDAP_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
VDAP/json (API)

# Install 'VDAP' in R:

install.packages('VDAP', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.15 score 14 scripts 155 downloads 17 exports 79 dependencies

Last updated from:b001b5399e. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	192
source / vignettes	OK	188
linux-release-x86_64	OK	156
wasm-release	OK	116

Exports:aaDist aaStruct Attrib Dups genPep hitSel KdA lcScan QCKd QCon resSep vComp.l vComp.lc vFormat vMotif.l vMotif.lc vSep

Dependencies:abind backports boot broom car carData cli codetools colorspace cowplot cpp11 Deriv doBy dplyr drc farver forecast Formula fracdiff generics ggplot2 glue gtable gtools isoband labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels mgcv microbenchmark minqa modelr multcomp mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig plotrix plyr purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang S7 sandwich scales SparseM stringi stringr survival TH.data tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr zoo

Help page	Topics
Position Independent Amino Acid Distributions	aaDist
Positional Amino Acid Composition Calculations	aaStruct
Calculate Peptide Length and Charge Attributes	Attrib
Average duplicated peptides from a VDAP dataset	Dups
Peptide generator based on the output of functions 'vComp' or 'vMotif'	genPep
Signal Based Hits Selection for VDAP	hitSel
Peptide Dissociation Rate Constant (Kd) Calculations	KdA
Signal or Kd Distributions separated by Length/Charge attributes	lcScan
Quality Control of Peptides Based on Reproducibility and Kd	QCKd
Subsetting for VDAP function QCKd	QCon
Select Peptides with the Specified Amino Acid Residue(s) at an Indicated Position	resSep
Amino Acid Disbutions by Position at Various Length/Charge	vComp vComp.l vComp.lc
Length/Charge/Kd Peptide Calculations and File Assembly	vFormat
Generate Signal Weighted Amino Acid Heat Maps by Position	vMotif vMotif.l vMotif.lc
Select Peptides of a Particular Length/Charge Combination	vSep

Package: VDAP 2.0.0

VDAP: Peptide Array Analysis Tools

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)