Package: HyPhy
Type: Package
Title: Macroevolutionary phylogentic analysis of species trees and gene
trees
Version: 1.0
Date: 2012-07-25
Authors@R: person("Nathaniel", "Hallinan", role = c("aut", "cre"),
email = "nmhallinan@gmail.com")
Author: Nathaniel Malachi Hallinan
Maintainer: Nathaniel Malachi Hallinan <nmhallinan@gmail.com>
Depends: ape, R.utils
Description: A Bay Area high level phylogenetic analysis package mostly
using the birth-death process. Analysis of species tree
branching times and simulation of species trees under a number
of different time variable birth-death processes. Analysis of
gene tree species tree reconciliations and simulations of gene
trees in species trees.
License: GPL-2
Packaged: 2012-07-29 23:15:47 UTC; Nat
Repository: CRAN
Date/Publication: 2012-07-30 04:09:01
Package: MSIseq
Maintainer: Mini Huang <mini.huang@nus.edu.sg>
License: GPL (>= 2)
Title: Assess Tumor Microsatellite Instability with a Decision Tree
Classifier from Exome Somatic Mutations
Type: Package
Author: Mini Huang
Description: A decision tree classifier for detecting microsatellite instability (MSI) in somatic mutation data from whole exome sequencing. MSI is detected based on different mutation rates in all sites as well as in simple sequence repeats. This mechanism can also be applied to sequence data of targeted gene panels with shorter sequence length.
SystemRequirements: Java
Version: 1.0.0
biocViews: Classification, SomaticMutation, Sequencing
Depends: IRanges, RWeka, rJava, R.utils, R (>= 3.2.0)
Date: 2015-06-10
NeedsCompilation: no
Packaged: 2015-06-15 12:10:59 UTC; minihuang
Repository: CRAN
Date/Publication: 2015-06-15 16:26:10
Package: PubBias
Type: Package
Title: Performs simulation study to look for publication bias, using a
technique described by Ioannidis and Trikalinos; Clin Trials.
2007;4(3):245-53.
Depends: rmeta, R.utils
Version: 1.0
Date: 2013-11-18
Author: Simon Thornley
Maintainer: Simon Thornley <sithor@gmail.com>
Description: I adapted a method designed by Ioannidis and Trikalinos, which
compares the observed number of positive studies in a meta-analysis with
the expected number, if the summary measure of effect, averaged over the
individual studies, were assumed true. Excess in the observed number of
positive studies, compared to the expected, is taken as evidence of
publication bias. The observed number of positive studies, at a given level
for statistical significance, is calculated by applying Fisher's exact test
to the reported 2x2 table data of each constituent study, doubling the
Fisher one-sided P-value to make a two-sided test. The corresponding
expected number of positive studies was obtained by summing the statistical
powers of each study. The statistical power depended on a given measure of
effect which, here, was the pooled odds ratio of the meta-analysis was
used. By simulating each constituent study, with the given odds ratio, and
the same number of treated and non-treated as in the real study, the power
of the study is estimated as the proportion of simulated studies that are
positive, again by a Fisher's exact test. The simulated number of events in
the treated and untreated groups was done with binomial sampling. In the
untreated group, the binomial proportion was the percentage of actual
events reported in the study and, in the treated group, the binomial
sampling proportion was the untreated percentage multiplied by the risk
ratio which was derived from the assumed common odds ratio. The statistical
significance for judging a positive study may be varied and large
differences between expected and observed number of positive studies around
the level of 0.05 significance constitutes evidence of publication bias.
The difference between the observed and expected is tested by chi-square. A
chi-square test P-value for the difference below 0.05 is suggestive of
publication bias, however, a less stringent level of 0.1 is often used in
studies of publication bias as the number of published studies is usually
small.
License: GPL-3
Collate: 'process.R'
Packaged: 2013-11-19 20:55:32 UTC; stho069
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-11-21 06:48:21
Package: acnr
Type: Package
Title: Annotated Copy-Number Regions
Version: 0.2.4
Date: 2014-10-27
Author: Morgane Pierre-Jean and Pierre Neuvial
Maintainer: Morgane Pierre-Jean <morgane.pierrejean@genopole.cnrs.fr>
Description: This data package contains SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.
License: LGPL (>= 2.1)
Depends: R (>= 2.10), R.utils, xtable
Repository: CRAN
Repository/R-Forge/Project: jointseg
Repository/R-Forge/Revision: 142
Repository/R-Forge/DateTimeStamp: 2014-11-17 15:27:15
Date/Publication: 2014-11-19 11:43:31
Packaged: 2014-11-17 15:45:28 UTC; rforge
NeedsCompilation: no
providing 
.