QuasiSeq: Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood

Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with 'QL', 'QLShrink' and 'QLSpline' methods (Lund, Nettleton, McCarthy, and Smyth, 2012).

Author
Steve Lund [aut], Long Qu [aut, cre, ctb], Ian Marschner [aut] (The author of glm2::glm.fit2, which was modified slightly leading to glm.fit3 in this package.), R Core Team [aut] (The author of stats::glm.fit, which was modified slightly leading to glm.fit3 in this package.)
Date of publication
2015-05-15 09:13:46
Maintainer
Long Qu <long.qu@wright.edu>
License
GPL (>= 2)
Version
1.0-8

View on CRAN

Man pages

NBDev
Fit a negative binomial GLM for given design matrix
PoisDev
Compute Poisson deviances (up to a constant) for given design...
QL.fit
Fit quasi-likelihood models to matrix of RNA-seq expression...
QL.results
Obtain p-values and q-values using results from 'QL.fit'

Files in this package

QuasiSeq
QuasiSeq/src
QuasiSeq/src/Makevars
QuasiSeq/src/uniqueNumericMatrix.cpp
QuasiSeq/src/registration.c
QuasiSeq/src/glmBias.c
QuasiSeq/NAMESPACE
QuasiSeq/R
QuasiSeq/R/coefglm.R
QuasiSeq/R/glmsolve.R
QuasiSeq/R/fbrNBglm.R
QuasiSeq/R/QL.results.R
QuasiSeq/R/glm.fit3.R
QuasiSeq/R/negbin.R
QuasiSeq/R/QL.fit.R
QuasiSeq/R/duplicated.matrix.R
QuasiSeq/R/NBDev.R
QuasiSeq/R/nlsolve.R
QuasiSeq/R/PoisDev.R
QuasiSeq/MD5
QuasiSeq/DESCRIPTION
QuasiSeq/man
QuasiSeq/man/QL.fit.Rd
QuasiSeq/man/NBDev.Rd
QuasiSeq/man/PoisDev.Rd
QuasiSeq/man/QL.results.Rd