SCORER2: SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences
Version 0.99.0

This package contains the functions necessary to run the SCORER 2.0 algorithm. SCORER 2.0 can be used to differentiate between parallel dimeric and trimeric coiled-coil sequence, which are the two most more frequent coiled-coil structures observed naturally. As such, SCORER 2.0 is particularly useful for researchers looking to characterize novel coiled-coil sequences. It may also be used to assist in the structural characterization of synthetic coiled-coil sequences. Also included in this package are functions that allows the user to retrain the SCORER 2.0 algorithm using user-defined training data.

Browse man pages Browse package API and functions Browse package files

AuthorCraig T. Armstrong, Thomas L. Vincent <tlfvincent@gmail.com>, Peter J. Green and Derek N. Woolfson <D.N.Woolfson@bristol.ac.uk>
Date of publication2014-01-17 06:10:40
MaintainerThomas L. Vincent <tlfvincent@gmail.com>
LicenseGPL (>= 2)
Version0.99.0
URL http://coiledcoils.chm.bris.ac.uk/Scorer/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SCORER2")

Man pages

CreatePssm: Compute profile scoring matrices for training data
EstimateProbability: Estimate oligomeric state score of coiled-coil sequences
pssm: Profile scoring matrix derived from the original SCORER 2.0...
RetrainScorer2: Retrain the SCORER 2.0 algorithm with user-defined training...
scorer2: Predict oligomerization state of coiled-coil sequences
scorer-package: Predict oligomerization state of coiled-coil sequences
training: Training dataset used to contruct the profile scoring matrix...

Functions

CreatePssm Man page Source code
EstimateProbability Man page Source code
RetrainScorer2 Man page Source code
pssm Man page
scorer2 Man page Source code
scorer2-package Man page
training Man page

Files

NAMESPACE
data
data/pssm.RData
data/training.RData
R
R/scorer2.R
R/RetrainScorer2.R
R/EstimateProbability.R
R/CreatePssm.R
MD5
DESCRIPTION
man
man/CreatePssm.Rd
man/scorer-package.Rd
man/EstimateProbability.Rd
man/training.Rd
man/scorer2.Rd
man/RetrainScorer2.Rd
man/pssm.Rd
SCORER2 documentation built on May 19, 2017, 2:58 p.m.