Package: Oscope
Type: Package
Title: Oscope - A statistical pipeline for identifying oscillatory
genes in unsynchronized single cell RNA-seq
Version: 1.2.0
Date: 2015-7-28
Author: Ning Leng
Maintainer: Ning Leng <lengning1@gmail.com>
Depends: EBSeq, cluster, testthat, BiocParallel
Suggests: BiocStyle
Description: Oscope is a statistical pipeline developed to identifying
and recovering the base cycle profiles of oscillating genes in
an unsynchronized single cell RNA-seq experiment. The Oscope
pipeline includes three modules: a sine model module to search
for candidate oscillator pairs; a K-medoids clustering module
to cluster candidate oscillators into groups; and an extended
nearest insertion module to recover the base cycle order for
each oscillator group.
License: Artistic-2.0
Collate: 'AbsCor.R' 'NormForSine.R' 'SineFun.R' 'FormatSineOut.R'
'Opt2Shift.R' 'SineOptim.R' 'PipeR.R' 'ImpShift.R'
'PipeShiftCDF.R' 'scanK.R' 'NISFun.R' 'CalcMV.R' 'OscopeKM.R'
'OscopeENI.R' 'OscopeSine.R' 'FlagCluster.R' 'PermuCut.R'
BuildVignettes: yes
biocViews: StatisticalMethod,RNASeq, Sequencing, GeneExpression
NeedsCompilation: no
Packaged: 2016-05-04 06:27:29 UTC; biocbuild
Package: EBSeqHMM
Type: Package
Title: Bayesian analysis for identifying gene or isoform expression
changes in ordered RNA-seq experiments
Version: 1.6.0
Date: 2015-03-21
Author: Ning Leng, Christina Kendziorski
Depends: EBSeq
Maintainer: Ning Leng <lengning1@gmail.com>
Description: The EBSeqHMM package implements an auto-regressive hidden Markov model for statistical analysis in ordered RNA-seq experiments (e.g. time course or spatial course data). The EBSeqHMM package provides functions to identify genes and isoforms that have non-constant expression profile over the time points/positions, and cluster them into expression paths.
License: Artistic-2.0
Collate: 'EBTest_ext.R' 'EBHMMNBfunForMulti.R' 'EBHMMNBfun.R'
'EBHMMNBMultiEM_2chain.R' 'f0.R' 'LikefunNBHMM.R' 'beta.mom.R'
'EBSeqHMMTest.R' 'GetConfidentCalls.R' 'GetDECalls.R'
'GetAllPaths.R' 'PlotExp.R'
BuildVignettes: yes
biocViews: StatisticalMethod, DifferentialExpression,
MultipleComparison, RNASeq, Sequencing, GeneExpression,
Bayesian, HiddenMarkovModel, TimeCourse
NeedsCompilation: no
Packaged: 2016-05-04 05:55:46 UTC; biocbuild
providing 
.