Guy Brock <guy.brock@louisville.edu>, Vasyl Pihur <vasyl.pihur@louisville.edu>,
Susmita Datta <susmita.datta@louisville.edu>, and
Somnath Datta <somnath.datta@louisville.edu>
R (>= 2.0), methods, cluster, kohonen, class, mclust
Statistical and biological validation of clustering results.

Guy Brock <guy.brock@louisville.edu>, Vasyl Pihur
<vasyl.pihur@louisville.edu>, Susmita Datta
<susmita.datta@louisville.edu>, and Somnath Datta
<somnath.datta@louisville.edu>
Biobase, annotate, GO.db, moe430a.db, RankAggreg, kohonen,
mclust
Statistical and biological validation of clustering
results.

Orphaned on 2018-02-21 as requested corrections were
not made.

Including unconditional use of Suggests package(s) from BioC.

Guy Brock <guy.brock@louisville.edu>, Vasyl Pihur <vpihur@gmail.com>,
Susmita Datta <susmita.datta@louisville.edu>, and
Somnath Datta <somnath.datta@louisville.edu>
Statistical and biological validation of clustering results. This package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and BSI. Further information can be found in Brock, G et al. (2008) <doi: 10.18637/jss.v025.i04>.

Biobase, BiocManager, annotate, GO.db, moe430a.db,
RankAggreg, kohonen, mclust

Clust Along Chromosomes, a method to call gains/losses in CGH
array data
Clust Along Chromosomes, a method to call gains/losses in
CGH array data

Clust Along Chromosomes, a method to call gains/losses in CGH array data
Pei Wang <wp57@stat.stanford.edu> , with contributions from Balasubramanian Narasimhan  <naras@stanford.edu>.

C++ implementations of phylogenetic calculations
Nicholas J. Matzke, Dept. of Integrative Biology, U.C. Berkeley
methods, Rcpp (>= 0.9.10), RcppArmadillo
This package implements in C++/Rcpp various
cladogenesis-related calculations that are slow in pure R.
These include the calculation of the probability of various
scenarios for the inheritance of geographic range at the
divergence events on a phylogenetic tree, and other
calculations necessary for models which are not continuous-time
markov chains (CTMC), but where change instead occurs
instantaneously at speciation events.  Typically these models
must assess the probability of every possible combination of
(ancestor state, left descendent state, right descendent
state).  This means that there are up to (# of states)^3
combinations to investigate, and in biogeographical models,
there can easily be hundreds of states, so calculation time
becomes an issue.  C++ implementation plus clever tricks (many
combinations can be eliminated a priori) can greatly speed the
computation time over naive R implementations.