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.

Author
Cody Moore
Date of publication
2016-05-22 22:54:19
Maintainer
Cody Moore <Jumper9400@gmail.com>
License
GPL-2
Version
2.0.0

View on CRAN

Man pages

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

Files in this package

VDAP
VDAP/NAMESPACE
VDAP/R
VDAP/R/QCKd_hitSel_0.1.0.R
VDAP/R/aaDist_0.1.0.R
VDAP/R/genPep_0.1.0.R
VDAP/R/vFormat_0.1.0.R
VDAP/R/resSep_0.2.0.R
VDAP/R/MPepGen0.0.1.R
VDAP/R/lcScan_1.2.8.R
VDAP/R/vSep_0.1.0.R
VDAP/R/Motifs_0.2.0.R
VDAP/MD5
VDAP/DESCRIPTION
VDAP/man
VDAP/man/lcScan.Rd
VDAP/man/vMotif.Rd
VDAP/man/resSep.Rd
VDAP/man/QCon.Rd
VDAP/man/Attrib.Rd
VDAP/man/genPep.Rd
VDAP/man/aaStruct.Rd
VDAP/man/QCKd.Rd
VDAP/man/vSep.Rd
VDAP/man/vComp.Rd
VDAP/man/aaDist.Rd
VDAP/man/Dups.Rd
VDAP/man/hitSel.Rd
VDAP/man/vFormat.Rd
VDAP/man/KdA.Rd