NBPSeq: Negative Binomial Models for RNA-Sequencing Data
Version 0.3.0

Negative Binomial (NB) models for two-group comparisons and regression inferences from RNA-Sequencing Data.

Browse man pages Browse package API and functions Browse package files

AuthorYanming Di <diy@stat.oregonstate.edu>, Daniel W Schafer <schafer@stat.oregonstate.edu>, with contributions from Jason S Cumbie <cumbiej@onid.orst.edu> and Jeff H Chang <changj@cgrb.oregonstate.edu>.
Date of publication2014-04-15 00:11:10
MaintainerYanming Di <diy@stat.oregonstate.edu>
LicenseGPL-2
Version0.3.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("NBPSeq")

Man pages

arab: Arabidopsis RNA-Seq Data Set
estimate.disp: Fit a parametric disperison model to thinned counts
estimate.dispersion: Estimate Negative Binomial Dispersion
estimate.norm.factors: Estiamte Normalization Factors
exact.nb.test: Exact Negative Binomial Test for Differential Gene Expression
irls.nb.1: Estimate the regression coefficients in an NB GLM model
nb.glm.test: Fit Negative Binomial Regression Model and Test for a...
NBPSeq-package: Negative Binomial Regression Models for Statistical Analysis...
nbp.test: NBP Test for Differential Gene Expression from RNA-Seq Counts
plot.nb.data: Boxplot and scatterplot matrix of relative frequencies (after...
plot.nb.dispersion: Plot the estimated dispersion as a function of the...
plot.nbp: Diagnostic Plots for an NBP Object
prepare.nb.data: Prepare the NB Data Structure for RNA-Seq Read Counts
prepare.nbp: Prepare the Data Structure for Exact NB test for Two-Group...
print.nb.data: Print summary of the nb counts
print.nb.dispersion: Print the estimated dispersion model
print.nbp: Print summary of an NBP Object
print.nb.test: Print output from 'test.coefficient'
test.coefficient: Large-sample Test for a Regression Coefficient in an Negative...

Functions

NBPSeq Man page
NBPSeq-package Man page
arab Man page
compute.tail.prob Source code
disp.nbp Source code
disp.nbq Source code
disp.nbs Source code
disp.step Source code
estimate.disp Man page Source code
estimate.dispersion Man page Source code
estimate.norm.factors Man page Source code
estimate.norm.factors.AH2010 Source code
exact.nb.test Man page Source code
example.smart.plot Source code
fit.nb.regression Source code
get.mean.hat Source code
get.nbp.pars Source code
get.rel.mean Source code
get.var.hat Source code
hoa.1d Source code
hoa.hd Source code
irls.nb Source code
irls.nb.1 Man page Source code
ll.nb Source code
ll.nb.2 Source code
log.phi.nb2 Source code
log.phi.nbp Source code
log.phi.nbq Source code
ma.plot Source code
mv.line Source code
mv.line.fitted Source code
mv.line.nbp Source code
mv.plot Source code
mv.points Source code
nb.glm.test Man page Source code
nbp.test Man page Source code
nll.log.phi.fun Source code
optim.disp.apl Source code
optim.disp.pl Source code
optim.pcl Source code
phi.line Source code
phi.line.fitted Source code
phi.line.nbp Source code
phi.plot Source code
plot.nb.data Man page Source code
plot.nb.dispersion Man page Source code
plot.nbp Man page Source code
plot.nbp.test Source code
prepare.nb.data Man page Source code
prepare.nbp Man page Source code
print.nb.data Man page Source code
print.nb.dispersion Man page Source code
print.nb.test Man page Source code
print.nbp Man page Source code
print.nbp.counts Source code
print.nbp.pars Source code
print.nbp.test Source code
smart.plot Source code
smart.points Source code
test.coefficient Man page Source code
test.compute.tail.prob Source code
test.log.likelihood Source code
thin.counts Source code

Files

inst
inst/examples
inst/examples/example.optim.pcl.R
inst/examples/example.test.coefficient.R
inst/examples/example.nbp.test.R
inst/examples/example.exact.nb.test.R
inst/examples/example.nb.glm.test.R
src
src/lm.c
NAMESPACE
data
data/arab.rda
R
R/plot.nb.data.R
R/nb.glm.optim.disp.R
R/normalization.R
R/nbp.classes.R
R/nbp.optim.disp.R
R/NBPSeq.package.R
R/nb.glm.dispersion.models.R
R/hoa.1d.R
R/nbp.main.R
R/nbp.exact.test.R
R/nb.glm.main.R
R/nbp.plots.R
R/nb.glm.R
R/hoa.hd.R
R/smart.plot.R
R/log.likelihood.R
MD5
DESCRIPTION
man
man/print.nb.dispersion.Rd
man/nbp.test.Rd
man/exact.nb.test.Rd
man/irls.nb.1.Rd
man/estimate.norm.factors.Rd
man/plot.nbp.Rd
man/prepare.nb.data.Rd
man/nb.glm.test.Rd
man/plot.nb.data.Rd
man/NBPSeq-package.Rd
man/arab.Rd
man/print.nb.data.Rd
man/print.nb.test.Rd
man/estimate.dispersion.Rd
man/plot.nb.dispersion.Rd
man/print.nbp.Rd
man/estimate.disp.Rd
man/test.coefficient.Rd
man/prepare.nbp.Rd
NBPSeq documentation built on May 20, 2017, 4:12 a.m.