Title: Efficiently Read Sequencing Data (VCF format, METAL format) into
R
Diff between seqminer versions 0.3 dated 2013-04-13 and 0.5 dated 2013-05-28
Description: Integrate sequencing data (VCF) or meta-analysis results
in R
Author: Xiaowei Zhan
Maintainer: Xiaowei Zhan
ChangeLog | 8 ++
DESCRIPTION | 6 +-
MD5 | 17 +++--
R/seqminer.R | 6 +-
man/readVCFToListByGene.Rd | 3 -
man/readVCFToListByRange.Rd | 3 -
src/RangeList.cpp | 13 ++--
src/RangeList.h | 79 +++++++++++++++++++-------
src/config.h |only
src/rvMetaLoader.cpp | 131 ++++++++++++++++++++++++++++++++++++++++++--
10 files changed, 219 insertions(+), 47 deletions(-)
Title: Sample size calculations for longitudinal data
Diff between longpower versions 1.0-7 dated 2013-05-22 and 1.0-8 dated 2013-05-28
Description: The longpower package contains functions for computing
power and sample size for linear models of longitudinal data
based on the formula due to Liu and Liang (1997) and Diggle et
al (2002). Either formula is expressed in terms of marginal
model or Generalized Estimating Equations (GEE) parameters.
This package contains functions which translate pilot mixed
effect model parameters (e.g. random intercept and/or slope)
into marginal model parameters so that the formulas of Diggle
et al or Liu and Liang formula can be applied to produce sample
size calculations for two sample longitudinal designs assuming
known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue
DESCRIPTION | 11 ++++++-----
MD5 | 2 +-
2 files changed, 7 insertions(+), 6 deletions(-)
Title: SBML Integration in Package sybil
Diff between sybilSBML versions 1.1.16 dated 2013-01-16 and 2.0.2 dated 2013-05-28
Description: SBML (Systems Biology Markup Language) integration in
sybil
Author: Gabriel Gelius-Dietrich [aut, cre], Deya Alzoubi [ctb]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 19 -
MD5 | 60 ++++-
NAMESPACE | 50 ++++
R/generics.R |only
R/readSBMLmod.R | 439 ++++++++++++++++----------------------
R/sbmlErrorClass.R |only
R/sbmlPtrClass.R |only
R/sybilSBML.R |only
R/uglyHack.R | 6
R/zzz.R |only
cleanup |only
configure |only
configure.ac |only
configure.win |only
inst/INSTALL |only
inst/NEWS.Rd | 54 ++++
inst/README |only
inst/doc/sybilSBML.R |only
inst/doc/sybilSBML.Rnw | 104 ++++-----
inst/doc/sybilSBML.pdf |binary
inst/extdata |only
man/closeSBMLfile.Rd |only
man/delSBMLmodel.Rd |only
man/getSBMLCompartList.Rd |only
man/getSBMLReactionsList.Rd |only
man/getSBMLSpeciesList.Rd |only
man/getSBMLerrors.Rd |only
man/getSBMLlevel.Rd |only
man/getSBMLmodId.Rd |only
man/getSBMLmodName.Rd |only
man/getSBMLmodel.Rd |only
man/getSBMLnumCompart.Rd |only
man/getSBMLnumReactions.Rd |only
man/getSBMLnumSpecies.Rd |only
man/getSBMLunitDefinitionsList.Rd |only
man/getSBMLversion.Rd |only
man/openSBMLfile.Rd |only
man/readSBMLmod.Rd | 37 +--
man/sbmlError-class.Rd |only
man/sbmlPtr-class.Rd |only
man/validateSBMLdocument.Rd |only
man/versionLibSBML.Rd |only
src |only
vignettes/sybilSBML.Rnw | 104 ++++-----
vignettes/sybilSBML.bib | 18 +
45 files changed, 484 insertions(+), 407 deletions(-)
Title: Dynamic time warping algorithms
Diff between dtw versions 1.15 dated 2012-08-22 and 1.16 dated 2013-05-28
Description: A comprehensive implementation of dynamic time warping
(DTW) algorithms in R. DTW computes the optimal (least
cumulative distance) alignment between points of two time
series. Common DTW variants covered include local (slope) and
global (window) constraints, subsequence matches, arbitrary
distance definitions, normalizations, minimum variance
matching, and so on. Provides cumulative distances,
alignments, specialized plot styles, etc.
Author: Toni Giorgino
Maintainer: Toni Giorgino
dtw-1.15/dtw/src/computeCM.h |only
dtw-1.16/dtw/DESCRIPTION | 23 ++--
dtw-1.16/dtw/MD5 | 40 +++----
dtw-1.16/dtw/NAMESPACE | 1
dtw-1.16/dtw/R/backtrack.R | 16 +-
dtw-1.16/dtw/R/dtw.R | 14 --
dtw-1.16/dtw/R/globalCostMatrix.R | 59 +++++-----
dtw-1.16/dtw/R/stepPattern.R | 7 -
dtw-1.16/dtw/inst/ChangeLog | 14 ++
dtw-1.16/dtw/inst/TODO | 22 ++-
dtw-1.16/dtw/inst/doc/dtw.pdf |binary
dtw-1.16/dtw/inst/dtw.bib |only
dtw-1.16/dtw/man/aami.Rd | 11 -
dtw-1.16/dtw/man/dtw-package.Rd | 41 ++++---
dtw-1.16/dtw/man/dtw.Rd | 57 +++++-----
dtw-1.16/dtw/man/dtwDist.Rd | 2
dtw-1.16/dtw/man/mvm.Rd | 3
dtw-1.16/dtw/man/stepPattern.Rd | 142 ++++++++++---------------
dtw-1.16/dtw/src/Makevars | 6 -
dtw-1.16/dtw/src/computeCM.c | 193 ++++++++++++++++++++++++++--------
dtw-1.16/dtw/tests/dtw_test.R | 9 +
dtw-1.16/dtw/tests/dtw_test.Rout.save | 13 ++
22 files changed, 406 insertions(+), 267 deletions(-)
Title: Nucleic Acid Melting Curve Analysis on Microbead Surfaces with R
Diff between MBmca versions 0.0.1 dated 2012-08-31 and 0.0.2 dated 2013-05-28
Description: The MBmca package provides data sets and lightweight
utilities for nucleic acid melting curve analysis and
presentation on microbead surfaces.
Author: Stefan Roediger
Maintainer: Stefan Roediger
CHANGELOG |only
DESCRIPTION | 11 +-
MD5 | 29 +++---
R/MFIerror.R | 25 +++--
R/diffQ.R | 183 +++++++++++++++++++++++++++++-----------
R/diffQ2.R | 107 ++++++++++++++---------
R/mcaPeaks.R |only
R/mcaSmoother.R | 96 ++++++++++++++-------
man/DMP.Rd | 52 +++++++----
man/DualHyb.Rd | 40 +++++---
man/MBmca-package.Rd | 28 +++---
man/MFIerror.Rd | 32 +++++--
man/MultiMelt.Rd | 80 ++++++++++-------
man/diffQ.Rd | 229 ++++++++++++++++++++++++++++++++++++++-------------
man/diffQ2.Rd | 211 ++++++++++++++++++++++++++++++++++++++++------
man/mcaPeaks.Rd |only
man/mcaSmoother.Rd | 182 +++++++++++++++++++++++++++++++++++-----
17 files changed, 961 insertions(+), 344 deletions(-)
Title: Treemap visualization
Diff between treemap versions 1.1-1 dated 2012-07-10 and 2.0.1 dated 2013-05-28
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw
treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes
treemap-1.1-1/treemap/R/baseTreemap.R |only
treemap-1.1-1/treemap/R/tmClick.R |only
treemap-1.1-1/treemap/R/tmLocate.R |only
treemap-1.1-1/treemap/data/sbsData.rda |only
treemap-1.1-1/treemap/man/sbsData.Rd |only
treemap-1.1-1/treemap/man/tmClick.Rd |only
treemap-1.1-1/treemap/man/tmLocate.Rd |only
treemap-2.0.1/treemap/DESCRIPTION | 25 -
treemap-2.0.1/treemap/MD5 | 50 +-
treemap-2.0.1/treemap/NAMESPACE | 7
treemap-2.0.1/treemap/NEWS | 17
treemap-2.0.1/treemap/R/cat2col.R | 18
treemap-2.0.1/treemap/R/comp2col.R | 4
treemap-2.0.1/treemap/R/createRec.R | 65 ++-
treemap-2.0.1/treemap/R/datasets.R | 9
treemap-2.0.1/treemap/R/dens2col.R | 4
treemap-2.0.1/treemap/R/depth2col.R |only
treemap-2.0.1/treemap/R/index2col.R | 29 +
treemap-2.0.1/treemap/R/overlap.R | 28 +
treemap-2.0.1/treemap/R/pkg.R | 21 -
treemap-2.0.1/treemap/R/tmAggregate.R |only
treemap-2.0.1/treemap/R/tmColorsLegend.R |only
treemap-2.0.1/treemap/R/tmDrawRect.R |only
treemap-2.0.1/treemap/R/tmGenerateRect.R |only
treemap-2.0.1/treemap/R/tmGetViewports.R |only
treemap-2.0.1/treemap/R/tmPlot.R | 503 ---------------------------
treemap-2.0.1/treemap/R/tmPrintTitles.R |only
treemap-2.0.1/treemap/R/treefunctions.R |only
treemap-2.0.1/treemap/R/treemap.R |only
treemap-2.0.1/treemap/R/value2col.R | 74 +--
treemap-2.0.1/treemap/Rprof.out |only
treemap-2.0.1/treemap/data/business.rda |only
treemap-2.0.1/treemap/man/business.Rd |only
treemap-2.0.1/treemap/man/tmPlot.Rd | 320 -----------------
treemap-2.0.1/treemap/man/treemap-package.Rd | 40 --
treemap-2.0.1/treemap/man/treemap.Rd |only
36 files changed, 225 insertions(+), 989 deletions(-)
Title: Simultaneous Confidence Interval for Multinomial Proportion
Diff between CoinMinD versions 1.0 dated 2013-04-23 and 1.1 dated 2013-05-28
Description: Methods for obtaining simultaneous confidence interval for
multinomial proportion have been proposed by many authors and
the present study include a variety of widely applicable
procedures. Seven classical methods (Wilson, Quesenberry and
Hurst, Goodman, Wald with and without continuity correction,
Fitzpatrick and Scott, Sison and Glaz) and Bayesian Dirichlet
models are included in the package. The advantage of MCMC pack
has been exploited to derive the Dirichlet posterior directly
and this also helps in handling the Dirichlet prior parameters.
This package is prepared to have equal and unequal values for
the Dirichlet prior distribution that will provide better scope
for data analysis and associated sensitivity analysis.
Author: Dr M.Subbiah
Maintainer: Sumathi
DESCRIPTION | 8 +--
MD5 | 38 ++++++++--------
NAMESPACE | 2
R/FS.R | 19 ++++++--
R/GM.R | 19 ++++++--
R/QH.R | 19 ++++++--
R/SG.R | 6 ++
R/WALD.R | 19 ++++++--
R/WALDCC.R | 19 ++++++--
R/WS.R | 20 ++++++--
man/BMDE.Rd | 39 ++--------------
man/BMDU.Rd | 46 -------------------
man/CoinMinD-package.Rd | 2
man/FS.Rd | 24 ++--------
man/GM.Rd | 25 +---------
man/QH.Rd | 27 +----------
man/SG.Rd | 114 +-----------------------------------------------
man/WALD.Rd | 25 +---------
man/WALDCC.Rd | 25 ----------
man/WS.Rd | 25 +---------
20 files changed, 158 insertions(+), 363 deletions(-)
Title: Rare Variant Tests
Diff between RVtests versions 1.1 dated 2013-01-20 and 1.2 dated 2013-05-28
Description: Use multiple regression methods to test rare variants
association with disease traits.
Author: C. Xu, and C. M. Greenwood
Maintainer: C. Xu
DESCRIPTION | 9 +++++----
MD5 | 34 +++++++++++++++++-----------------
R/LASSO.R | 2 +-
R/PCR.R | 3 ++-
R/PLS.R | 3 ++-
R/RR.R | 9 +++++++--
R/SPLS.R | 2 +-
R/VTWOD.R | 3 ++-
R/geno2count.R | 8 ++++++--
man/LASSO.Rd | 7 +++++--
man/PCR.Rd | 6 +++++-
man/PLS.Rd | 6 +++++-
man/RR.Rd | 6 +++++-
man/RVtests-package.Rd | 7 +++++--
man/SPLS.Rd | 10 +++++++---
man/VTWOD.Rd | 7 +++++--
man/count2geno.Rd | 4 ++--
man/geno2count.Rd | 4 ++--
18 files changed, 84 insertions(+), 46 deletions(-)
Title: CoreArray Genomic Data Structure (GDS) R Interface
Diff between gdsfmt versions 0.9.13 dated 2013-05-20 and 0.9.14 dated 2013-05-28
Description: CoreArray project is to develop portable and scalable
storage technologies for bioinformatics data, allowing parallel
computing at the multicore and cluster levels.
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 8 ++--
MD5 | 78 ++++++++++++++++++++---------------------
NEWS | 5 ++
inst/CITATION | 2 -
inst/doc/CoreArrayTutorial.pdf |binary
man/add.gdsn.Rd | 2 -
man/addfile.gdsn.Rd | 11 +++--
man/append.gdsn.Rd | 2 -
man/apply.gdsn.Rd | 2 -
man/assign.gdsn.Rd | 2 -
man/cleanup.gds.Rd | 2 -
man/closefn.gds.Rd | 2 -
man/clusterApply.gdsn.Rd | 2 -
man/cnt.gdsn.Rd | 2 -
man/compression.gdsn.Rd | 2 -
man/createfn.gds.Rd | 5 +-
man/delete.attr.gdsn.Rd | 2 -
man/delete.gdsn.Rd | 2 -
man/gds.class.Rd | 5 +-
man/gdsUnitTest.Rd | 2 -
man/gdsfmt-package.Rd | 29 +++++++--------
man/gdsn.class.Rd | 2 -
man/get.attr.gdsn.Rd | 2 -
man/getfile.gdsn.Rd | 2 -
man/index.gdsn.Rd | 2 -
man/lasterr.gds.Rd | 2 -
man/ls.gdsn.Rd | 2 -
man/name.gdsn.Rd | 2 -
man/objdesp.gdsn.Rd | 2 -
man/openfn.gds.Rd | 2 -
man/print.gds.class.Rd | 2 -
man/print.gdsn.class.Rd | 2 -
man/put.attr.gdsn.Rd | 2 -
man/read.gdsn.Rd | 2 -
man/readex.gdsn.Rd | 2 -
man/readmode.gdsn.Rd | 2 -
man/rename.gdsn.Rd | 2 -
man/setdim.gdsn.Rd | 2 -
man/sync.gds.Rd | 2 -
man/write.gdsn.Rd | 2 -
40 files changed, 108 insertions(+), 97 deletions(-)