tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions
Version 1.22.0

Differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

Browse man pages Browse package API and functions Browse package files

AuthorJuan R Gonzalez <jrgonzalez@creal.cat> and Mikel Esnaola <mesnaola@creal.cat> (with contributions from Robert Castelo <robert.castelo@upf.edu>)
Bioconductor views DifferentialExpression RNASeq Sequencing StatisticalMethod
Date of publicationNone
MaintainerJuan R Gonzalez <jrgonzalez@creal.cat>
LicenseGPL (>= 2)
Version1.22.0
URL http://www.creal.cat/jrgonzalez/software.htm
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("tweeDEseq")

Man pages

compareCountDistributions: Compare count data distributions
distPoissonTweedie: The Poisson-Tweedie family of distributions
filterCounts: Count data filtering
glmPT: Fit Poisson-Tweedie generalized linear model.
gofTest: Test the goodness of fit of every row in a matrix of counts
mlePoissonTweedie: Maximum likelihood estimation of the Poisson-Tweedie...
normalizeCounts: Count data normalization
print.mlePT: Methods for objects of class 'mlePT'
qqchisq: Chi-square quantile-quantile plot
seizure: Epileptic seizure counts
testShapePT: Test shape parameter of PT
tweeDE: Score test for differences between two Poisson-Tweedie groups
tweeDEseq-internal: Internal 'tweeDEseq' functions
tweeDExact: Exact test for differences between two Poisson-Tweedie groups

Functions

AIC.glmPT Source code
L Source code
MAplot Man page Source code
MAplot.tweeDE Man page Source code
Vplot Man page Source code
Vplot.tweeDE Man page Source code
anova.glmPT Source code
compareCountDist Man page Source code
confint.mlePT Man page Source code
dPT Man page Source code
exactTestPT Man page Source code
filterCounts Man page Source code
gammratio Source code
getParam Man page Source code
getZhuParam Source code
glmPT Man page Source code
glmPT.fit Man page Source code
gofTest Man page Source code
hou2puig Source code
k Source code
k3 Source code
kappa3 Source code
kvector Source code
logLik.glmPT Source code
logLik.mlePT Man page Source code
loglikGlmPT Man page Source code
loglikPoissonTweedie Man page Source code
loglikPoissonTweedie2 Man page Source code
loglikPoissonTweedie3 Source code
mlePT Man page
mlePoissonTweedie Man page Source code
momentEstimates Man page Source code
normalizeCounts Man page Source code
onLoad Source code
onUnload Source code
print.glmPT Source code
print.mlePT Man page Source code
print.tweeDE Man page Source code
puig2hou Source code
qqchisq Man page Source code
rPT Man page Source code
sPackageLoaded Source code
seizure Man page
shapeTrend Man page Source code
summary.glmPT Source code
testPoissonTweedie Man page Source code
testShapePT Man page Source code
tweeDE Man page Source code
tweeDEglm Man page Source code
tweeDEseq-internal Man page
tweeDExact Man page Source code
zhu2hou Source code

Files

DESCRIPTION
NAMESPACE
R
R/L.R
R/MAplot.tweeDE.R
R/Vplot.tweeDE.R
R/compareCountDist.R
R/confint.mlePT.R
R/dPT.R
R/exactTestPT.R
R/firstlib.R
R/gammratio.R
R/getParam.R
R/glmPT.R
R/gofTest.R
R/logLik.mlePT.R
R/loglikGlmPT.R
R/loglikPoissonTweedie.R
R/mlePoissonTweedie.R
R/momentEstimates.R
R/normalizeCounts.R
R/parameterization.R
R/print.mlePT.R
R/print.tweeDE.R
R/qqchisq.R
R/rPT.R
R/shapeTrend.R
R/testPoissonTweedie.R
R/testShapePT.R
R/tweeDE.R
R/tweeDEglm.R
R/tweeDExact.R
build
build/vignette.rds
data
data/seizure.rda
inst
inst/CITATION
inst/doc
inst/doc/tweeDEseq.R
inst/doc/tweeDEseq.Rnw
inst/doc/tweeDEseq.pdf
man
man/compareCountDistributions.Rd
man/distPoissonTweedie.Rd
man/filterCounts.Rd
man/glmPT.Rd
man/gofTest.Rd
man/mlePoissonTweedie.Rd
man/normalizeCounts.Rd
man/print.mlePT.Rd
man/qqchisq.Rd
man/seizure.Rd
man/testShapePT.Rd
man/tweeDE.Rd
man/tweeDEseq-internal.Rd
man/tweeDExact.Rd
src
src/cov_wt_C.c
src/init_tweeDEseq.c
src/loglikGlm.c
src/logprobs.c
src/permtest.c
src/probs.c
src/tweeDEseq.h
src/zhu2.c
src/zhu3.c
vignettes
vignettes/tweeDEseq.Rnw
vignettes/tweeDEseq.bib
tweeDEseq documentation built on May 20, 2017, 10:32 p.m.