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-4.5-noble)VDAP_2.0.0.tar.gz(r-4.4-noble)
VDAP_2.0.0.tgz(r-4.4-emscripten)VDAP_2.0.0.tgz(r-4.3-emscripten)
VDAP.pdf |VDAP.html✨
VDAP/json (API)

# Install 'VDAP' in R:

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

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 117 downloads 17 exports 71 dependencies

Last updated 9 years agofrom:b001b5399e. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 20 2024
R-4.5-linux	OK	Nov 20 2024

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 fansi farver Formula generics ggplot2 glue gtable gtools isoband labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels mgcv microbenchmark minqa modelr multcomp munsell mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig plotrix plyr purrr quantreg R6 RColorBrewer Rcpp RcppEigen reshape2 rlang sandwich scales SparseM stringi stringr survival TH.data tibble tidyr tidyselect 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)