Package: MetaQC
Type: Package
Title: MetaQC: Objective Quality Control and Inclusion/Exclusion
Criteria for Genomic Meta-Analysis
Version: 0.1.13
Author: Don Kang <donkang75@gmail.com> and George Tseng
<ctseng@pitt.edu>
Maintainer: Don Kang <donkang75@gmail.com>
Description: MetaQC implements our proposed quantitative quality
control measures: (1) internal homogeneity of co-expression
structure among studies (internal quality control; IQC); (2)
external consistency of co-expression structure correlating
with pathway database (external quality control; EQC); (3)
accuracy of differentially expressed gene detection (accuracy
quality control; AQCg) or pathway identification (AQCp); (4)
consistency of differential expression ranking in genes
(consistency quality control; CQCg) or pathways (CQCp). (See
the reference for detailed explanation.) For each quality
control index, the p-values from statistical hypothesis testing
are minus log transformed and PCA biplots were applied to
assist visualization and decision. Results generate systematic
suggestions to exclude problematic studies in microarray
meta-analysis and potentially can be extended to GWAS or other
types of genomic meta-analysis. The identified problematic
studies can be scrutinized to identify technical and biological
causes (e.g. sample size, platform, tissue collection,
preprocessing etc) of their bad quality or irreproducibility
for final inclusion/exclusion decision.
Depends: R (>= 2.10.0), proto, foreach, iterators
Suggests: doMC, doSNOW, FactoMineR, matrixStats, gdata, gtools, survival
License: GPL-2
URL: https://github.com/donkang75/MetaQC
LazyLoad: yes
Collate: MetaQC.R requireAll.R functions.R runQC.R cleanup.R
Date: 2012-12-21
Packaged: 2012-12-21 22:10:50 UTC; ddkang
Repository: CRAN
Date/Publication: 2012-12-22 07:39:42
Package: PKgraph
Title: Model diagnostics for population pharmacokinetic models
Version: 1.7
Date: 2012-03-12
Depends: R (>= 2.10.0), RGtk2, gWidgetsRGtk2, cairoDevice, lattice, rggobi, ggplot2, proto
Imports: RGtk2, gWidgetsRGtk2
Author: Xiaoyong Sun
Maintainer: Xiaoyong Sun <johnsunx1@gmail.com>
Description: PKgraph provides a graphical user interface for population
pharmacokinetic model diagnosis. It also provides an integrated
and comprehensive platform for the analysis of pharmacokinetic
data including exploratory data analysis, goodness of model
fit, model validation and model comparison. Results from a
variety of modeling fitting software, including NONMEM,
Monolix, SAS and R, can be used. PKgraph is programmed in R,
and uses the R packages lattice, ggplot2 for static graphics,
and rggobi for interactive graphics.
License: GPL (>= 2)
LazyData: true
Collate: global.r psnCdd.r psnBootstrap.r functionOK.r proto.r ggobi.r
function.r handler.r PKgraphlayout.r PKgraph.r
Repository: CRAN
Date/Publication: 2012-03-14 06:21:01
Packaged: 2012-03-14 02:09:10 UTC; sunx1
Package: SparseFactorAnalysis
Type: Package
Title: Scaling Count and Binary Data with Sparse Factor Analysis
Version: 1.0
Date: 2015-07-20
Author: Marc Ratkovic, In Song Kim, John Londregan, and Yuki Shiraito
Maintainer: Marc Ratkovic <ratkovic@princeton.edu>
Description: Multidimensional scaling provides a means of uncovering a latent structure underlying observed data, while estimating the number of latent dimensions. This package presents a means for scaling binary and count data, for example the votes and word counts for legislators. Future work will include an EM implementation and extend this work to ordinal and continuous data.
License: GPL (>= 2)
Depends: directlabels, proto, ggplot2
Imports: Rcpp (>= 0.11.4), MASS, VGAM, truncnorm
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2015-07-23 03:06:28 UTC; ratkovic
Repository: CRAN
Date/Publication: 2015-07-23 07:05:04
Package: R2STATS
Type: Package
Title: A GTK GUI for fitting and comparing GLM and GLMM in R
Version: 0.68-38
Encoding: UTF-8
Date: 2013-10-02
Author: Yvonnick Noel
Maintainer: Yvonnick Noel <yvonnick.noel@uhb.fr>
Description: R2STATS is a gWidgetsRGtk2 GUI for fitting and comparing GLM or GLMM (based on Douglas Bates' lme4 package) in R. It is designed to make comparisons between numerous models easy, both numerically and graphically, which may be useful for teaching. Relevant plots are automatically produced for each model family. R2STATS is *not* a generic graphical interface for R, but a GUI for statistical modelling in a model comparison approach.
URL: http://yvonnick.noel.free.fr/r2stats
License: GPL (>= 2)
Depends: R (>= 2.14.0), proto, Matrix
Imports: grDevices, lattice, lme4, cairoDevice, gWidgets, gWidgetsRGtk2, RGtk2Extras, MASS, utils, latticeExtra, statmod
Repository: CRAN
Repository/R-Forge/Project: r2stats
Repository/R-Forge/Revision: 52
Repository/R-Forge/DateTimeStamp: 2014-04-21 10:14:23
Date/Publication: 2014-04-22 12:07:26
Packaged: 2014-04-21 12:18:56 UTC; rforge
NeedsCompilation: no
Package: AtelieR
Type: Package
Title: A GTK GUI for teaching basic concepts in statistical inference,
and doing elementary bayesian tests.
Version: 0.24
Encoding: UTF-8
Date: 2013-09-22
Author: Yvonnick Noel
Maintainer: Yvonnick Noel <yvonnick.noel@uhb.fr>
Description: A collection of statistical simulation and computation tools with a GTK GUI, to help teach statistical concepts and compute probabilities. Two domains are covered: I. Understanding (Central-Limit Theorem and the Normal Distribution, Distribution of a sample mean, Distribution of a sample variance, Probability calculator for common distributions), and II. Elementary Bayesian Statistics (bayesian inference on proportions, contingency tables, means and variances, with informative and noninformative priors).
License: GPL (>= 2)
Depends: R (>= 2.10), proto, cairoDevice, gWidgetsRGtk2, partitions
Packaged: 2013-09-22 10:29:34 UTC; noel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-09-22 12:47:09
Package: gsubfn
Version: 0.6-6
Date: 2014-08-23
Title: Utilities for strings and function arguments.
Author: G. Grothendieck
Maintainer: G. Grothendieck <ggrothendieck@gmail.com>
Description: gsubfn is like gsub but can take a replacement function
or certain other objects instead of the replacement string.
Matches and back references are input to the replacement function and
replaced by the function output. gsubfn can be used to split strings
based on content rather than delimiters and for quasi-perl-style string
interpolation. The package also has facilities for translating formulas
to functions and allowing such formulas in function calls instead of
functions. This can be used with R functions such as apply, sapply,
lapply, optim, integrate, xyplot, Filter and any other function that
expects another function as an input argument or functions like cat
or sql calls that may involve strings where substitution is desirable.
ByteCompile: true
Depends: R (>= 2.15.0), proto
Suggests: boot, chron, doBy, grid, lattice, quantreg, reshape, svUnit, tcltk, zoo
License: GPL (>= 2)
URL: http://gsubfn.googlecode.com
Packaged: 2014-08-23 12:40:54 UTC; Louis
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-27 21:17:14
Package: argparse
Type: Package
Title: Command line optional and positional argument parser.
Version: 1.0.1
Author: Trevor L Davis. Ports examples from the argparse Python module by the
Python Software Foundation. Ports examples from the getopt package by Allen
Day.
Maintainer: Trevor L Davis <trevor.l.davis@stanford.edu>
Description: A command line parser to
be used with Rscript to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
License: GPL (>= 2)
Copyright: See file (inst/)COPYRIGHTS.
URL: https://github.com/trevorld/argparse
BugReports: https://github.com/trevorld/argparse/issues
LazyLoad: yes
Depends: proto
Imports: findpython, getopt (>= 1.19), rjson
SystemRequirements: python (>= 2.7)
Suggests: knitr, testthat
VignetteBuilder: knitr
Packaged: 2014-04-04 19:51:16 UTC; trevorld
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-05 08:05:30
Package: benchmark
Type: Package
Title: Benchmark Experiments Toolbox
Version: 0.3-6
Date: 2014-05-02
Authors@R: c(person("Manuel", "J. A. Eugster", role = c("aut", "cre"),
email = "manuel@mjae.net"))
Depends: R (>= 2.10), utils, proto, ggplot2, relations, psychotools
Imports: reshape, scales, plyr
Suggests: coin, multcomp, lme4, e1071, entropy, archetypes, Rgraphviz, psychotree
Description: The benchmark package provides a toolbox for setup, execution
and analysis of benchmark experiments. Main focus is the analysis of
data accumulating during the execution -- one primary objective is the
statistical correct computation of the candidate algorithms' order.
License: GPL (>= 2)
URL: http://benchmark.r-forge.r-project.org/
Collate: 'algperf-beplot0.R' 'testprocedure.R' 'proto.R'
'algperf-paircomp.R' 'algperf-preference.R'
'algperf-visualizations.R' 'warehouse.R' 'algperf.R'
'as.psychobench.R' 'as.warehouse.R' 'benchmark.R' 'bsgraph.R'
'bsplot.R' 'datachar-visualizations.R'
'dataset-characteristics.R' 'dataset.R'
'dataset-characterization.R' 'testres-analysis.R'
'testres-visualizations.R'
Packaged: 2014-05-02 19:33:37 UTC; eugstem1
Author: Manuel J. A. Eugster [aut, cre]
Maintainer: Manuel J. A. Eugster <manuel@mjae.net>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-02 21:48:47
providing 
.