Package: protr
Version: 0.2-0
Date: 2013-12-10
Title: Protein Sequence Descriptor Calculation and Similarity
Computation with R
Description: The protr package focus on offering a unique and comprehensive
toolkit for protein sequence descriptor calculation and similarity
computation. The descriptors included in the protr package are extensively
utilized in Bioinformatics and Chemogenomics research. The qualitative
descriptors listed in protr include Amino Acid Composition (Amino Acid
Composition/Dipeptide Composition/Tripeptide Composition) descriptor,
Autocorrelation (Normalized Moreau-Broto Autocorrelation/Moran
Autocorrelation/Geary Autocorrelation) descriptor, CTD
(Composition/Transition/Distribution) descriptor, Conjoint Traid
descriptor, Quasi-sequence Order (Sequence Order Coupling
Number/Quasi-sequence Order Descriptors) descriptor and Pseudo Amino Acid
Composition (Pseudo Amino Acid Composition/Amphiphilic Pseudo Amino Acid
Composition) descriptor. The quantitative descriptors, for
Proteochemometric (PCM) Modeling, includes the Generalized Scales-Based
Descriptors derived by Principal Components Analysis, Generalized
Scales-Based Descriptors derived by AA-Properties (AAindex), Generalized
Scales-Based Descriptors derived by 20+ classes of 2D and 3D Molecular
Descriptors (Topological, WHIM, VHSE, etc.), Generalized Scales-Based
Descriptors derived by Factor Analysis, Generalized Scales-Based
Descriptors derived by Multidimensional Scaling, and Generalized BLOSUM/PAM
Matrix-Derived Descriptors. The protr package also integrates the
functionality of parallellized similarity computation derived by protein
sequence alignment and Gene Ontology (GO) semantic similarity measures
between a list of protein sequences / GO terms / Entrez Gene IDs. ProtrWeb,
the web service built on protr, is located at:
http://cbdd.csu.edu.cn:8080/protrweb/ . The protr package is developed by
Computational Biology and Drug Design (CBDD) Group, Central South
University.
Author: Nan Xiao <road2stat@gmail.com>, Qingsong Xu <dasongxu@gmail.com>,
Dongsheng Cao <oriental-cds@163.com>
Maintainer: Nan Xiao <road2stat@gmail.com>
License: BSD 3-clause License
URL: https://github.com/road2stat/protr/
BugReports: https://github.com/road2stat/protr/issues
LazyData: yes
Suggests: Biostrings, GOSemSim, foreach, doParallel, doMC
Packaged: 2013-12-19 06:58:46 UTC; jimmy
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-19 09:31:24