timeSeq: Detecting Differentially Expressed Genes in Time Course RNA-Seq Data

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Uses a negative binomial mixed-effects (NBME) model to detect nonparallel differential expression(NPDE) genes and parallel differential expression(PDE) genes in the time course RNA-seq data.

Author
Fan Gao, Xiaoxiao Sun
Date of publication
2016-10-28 00:05:29
Maintainer
Fan Gao <fangaohz@gmail.com>
License
GPL (>= 2)
Version
1.0.2

View on CRAN

Man pages

pAbp
Example Data in Vignette
simulate.dt
Example Data in Vignette
timeSeq
Statistical Inference for Time Course RNA-Seq Data using a...
timeSeq_1.0.2-package
Statistical Inference for Time Course RNA-Seq Data using a...
timeSeq.heatmap
Heatmap of the Most Significant NDPE Genes
timeSeq.permutate
Bootstrap method for Significance Testing of NPDE genes
timeSeq.screeplot
Scree Plot of Kullback Leibler Distance Ratios
timeSeq.sort
Sort NDPE Genes by Kullback Leibler Distance Ratios

Files in this package

timeSeq
timeSeq/inst
timeSeq/inst/doc
timeSeq/inst/doc/my-vignette.html
timeSeq/inst/doc/my-vignette.Rmd
timeSeq/inst/doc/my-vignette.R
timeSeq/NAMESPACE
timeSeq/data
timeSeq/data/simulate.dt.RData
timeSeq/data/pAbp.RData
timeSeq/R
timeSeq/R/timeSeq.R
timeSeq/R/timeSeq.sort.R
timeSeq/R/timeSeq.permutate.R
timeSeq/R/timeSeq.heatmap.R
timeSeq/R/timeSeq.screeplot.R
timeSeq/vignettes
timeSeq/vignettes/heatmap.png
timeSeq/vignettes/scree.png
timeSeq/vignettes/my-vignette.Rmd
timeSeq/MD5
timeSeq/build
timeSeq/build/vignette.rds
timeSeq/DESCRIPTION
timeSeq/man
timeSeq/man/timeSeq.screeplot.Rd
timeSeq/man/simulate.dt.Rd
timeSeq/man/timeSeq_1.0.2-package.Rd
timeSeq/man/timeSeq.permutate.Rd
timeSeq/man/timeSeq.heatmap.Rd
timeSeq/man/timeSeq.sort.Rd
timeSeq/man/pAbp.Rd
timeSeq/man/timeSeq.Rd