tcgsaseq: Time-Course Gene Set Analysis for RNA-Seq Data
Version 1.4.1

Gene set analysis of longitudinal RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights. Method is detailed in: Agniel D, Hejblum BP (2016) Variance component score test for time-course gene set analysis of longitudinal RNA-seq data .

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AuthorDenis Agniel [aut], Boris P. Hejblum [aut, cre]
Date of publication2017-02-21 23:11:17
MaintainerBoris P. Hejblum <boris.hejblum@u-bordeaux.fr>
LicenseGPL-2 | file LICENSE
Version1.4.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("tcgsaseq")

Man pages

baduel_5gs: Small portion of RNA-seq data from plant physiology study.
compute_sim_voomlike: Computing simulations results
compute_sim_voomlike_genewise: Computing simulations results observation-wise
data_sim_voomlike: Data simulation function
deseq_fn: Computes gen-wise pvals from DESeq2 method using...
grapes-pow-grapes: Power for matrix elements
nb_sim_fn: Computing negative binomial simulations results
nonlin_sim_fn: Computing nonlinear simulations results
PBT_gmt: PBT gene sets related to kidney transplant
qAbundanceDist: Gene abundance proportion distribution of RNA-seq data.
sp_weights: Non parametric local heteroscedasticity weights
tcgsaseq: tcgsaseq: a package to perform Time-course Gene Set Analysis...
tcgsa_seq: Time-course Gene Set Analyis
vc_score: Computes variance component test statistic for longitudinal
vc_score_h: Computes variance component test statistic for homogeneous...
vc_test_asym: Computes variance component test statistic for longitudinal
vc_test_perm: Permutation-based variance component test statistic for...
voom_weights: Precision weights accounting for heteroscedasticity in...

Functions

Kappa_j Source code
PBT Man page
PBT_gmt Man page
\%^\% Man page
baduel Man page
baduel_5gs Man page
baduel_gmt Man page
compute_sim_voomlike Man page Source code
compute_sim_voomlike_genewise Man page Source code
data_sim_voomlike Man page Source code
deseq_fn Man page Source code
deseq_fn_gs Source code
design Man page
expr_norm_corr Man page
nb_sim_fn Man page Source code
nonlin_sim_fn Man page Man page Source code Source code
qAbundanceDist Man page
sim_nb_data Source code
sim_nonlin_data Source code
sp_weights Man page Source code
tcgsa_seq Man page Source code
tcgsaseq Man page
tcgsaseq-package Man page
vc_score Man page Source code
vc_score_h Man page Source code
vc_test_asym Man page Source code
vc_test_perm Man page Source code
voom_weights Man page Source code

Files

inst
inst/CITATION
NAMESPACE
NEWS
data
data/qAbundanceDist.RData
data/baduel_5gs.RData
data/datalist
data/PBT_gmt.RData
R
R/vc_score_h.R
R/deseq_fn.R
R/compute_sim_voomlike_genewise.R
R/qAbundanceDist.R
R/compute_nonlin_sim.R
R/compute_sim_voomlike.R
R/baduel.R
R/tcgsa_seq.R
R/voom_weights.R
R/sp_weights.R
R/vc_score.R
R/PBT_gmt.R
R/data_sim_voomlike.R
R/compute_nonlin_gene_sim.R
R/vc_test_asym.R
R/compute_nb_sim.R
R/vc_test_perm.R
R/TcGSAseq-package.R
R/TcGSAseq_internal.R
MD5
README
DESCRIPTION
man
man/PBT_gmt.Rd
man/compute_sim_voomlike_genewise.Rd
man/voom_weights.Rd
man/tcgsa_seq.Rd
man/baduel_5gs.Rd
man/vc_score_h.Rd
man/vc_test_asym.Rd
man/data_sim_voomlike.Rd
man/grapes-pow-grapes.Rd
man/nb_sim_fn.Rd
man/vc_test_perm.Rd
man/compute_sim_voomlike.Rd
man/deseq_fn.Rd
man/vc_score.Rd
man/nonlin_sim_fn.Rd
man/sp_weights.Rd
man/tcgsaseq.Rd
man/qAbundanceDist.Rd
LICENSE
tcgsaseq documentation built on May 20, 2017, 5:40 a.m.