:: DESCRIPTION
PHYBASE provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees (gene trees and species trees).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics, 26 (7), 962-3 2010 Apr 1
Phybase: An R Package for Species Tree Analysis
Liang Liu 1, Lili Yu
:: DESCRIPTION
VRMLGen is a free R software package to generate 3D representations of biological data in the Virtual Reality Markup Language
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor
vrmlgen: An R Package for 3D Data Visualization on the Web
Journal of Statistical Software, 2010 DOI: 10.18637/jss.v036.i08
:: DESCRIPTION
The apcluster package implements Frey’s and Dueck’s Affinity Propagation clustering in R. The algorithms are largely analogous to the Matlab code published by Frey and Dueck. The package further provides an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results
::DEVELOPER
Institute of Bioinformatics, Johannes Kepler University Linz
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
U. Bodenhofer, A. Kothmeier, and S. Hochreiter (2011).
APCluster: an R package for affinity propagation clustering.
Bioinformatics 27:2463-2464
:: DESCRIPTION
The KeBABS package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define similarity measures between sequences.
::DEVELOPER
Institute of Bioinformatics, Johannes Kepler University Linz
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
KeBABS: an R package for kernel-based analysis of biological sequences.
Palme J, Hochreiter S, Bodenhofer U.
Bioinformatics. 2015 Mar 25. pii: btv176.
:: DESCRIPTION
Rseg allows the user to define sample-specific thresholds to call gains and losses in an interactive way. It also allows the user to correct for RMA induced normalization artifacts in case of imbalance between losses and gains.
::DEVELOPER
Lamy P (plamy@cs.au.dk), Wiuf C, Ørntoft TF, Andersen CL.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rseg–an R package to optimize segmentation of SNP array data.
Lamy P, Wiuf C, Ørntoft TF, Andersen CL.
Bioinformatics. 2011 Feb 1;27(3):419-20.
