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

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Gene set analysis of longitudinal RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights.

Author
Denis Agniel [aut], Boris P. Hejblum [aut, cre]
Date of publication
2016-11-24 16:39:19
Maintainer
Boris P. Hejblum <boris.hejblum@u-bordeaux.fr>
License
GPL-2 | file LICENSE
Version
1.3.1

View on CRAN

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...

Files in this package

tcgsaseq
tcgsaseq/inst
tcgsaseq/inst/CITATION
tcgsaseq/NAMESPACE
tcgsaseq/NEWS
tcgsaseq/data
tcgsaseq/data/qAbundanceDist.RData
tcgsaseq/data/baduel_5gs.RData
tcgsaseq/data/datalist
tcgsaseq/data/PBT_gmt.RData
tcgsaseq/R
tcgsaseq/R/vc_score_h.R
tcgsaseq/R/deseq_fn.R
tcgsaseq/R/compute_sim_voomlike_genewise.R
tcgsaseq/R/qAbundanceDist.R
tcgsaseq/R/compute_nonlin_sim.R
tcgsaseq/R/compute_sim_voomlike.R
tcgsaseq/R/baduel.R
tcgsaseq/R/tcgsa_seq.R
tcgsaseq/R/voom_weights.R
tcgsaseq/R/sp_weights.R
tcgsaseq/R/vc_score.R
tcgsaseq/R/tcgsaseq_internal.R
tcgsaseq/R/PBT_gmt.R
tcgsaseq/R/data_sim_voomlike.R
tcgsaseq/R/compute_nonlin_gene_sim.R
tcgsaseq/R/vc_test_asym.R
tcgsaseq/R/compute_nb_sim.R
tcgsaseq/R/vc_test_perm.R
tcgsaseq/R/TcGSAseq-package.R
tcgsaseq/MD5
tcgsaseq/README
tcgsaseq/DESCRIPTION
tcgsaseq/man
tcgsaseq/man/PBT_gmt.Rd
tcgsaseq/man/compute_sim_voomlike_genewise.Rd
tcgsaseq/man/voom_weights.Rd
tcgsaseq/man/tcgsa_seq.Rd
tcgsaseq/man/baduel_5gs.Rd
tcgsaseq/man/vc_score_h.Rd
tcgsaseq/man/vc_test_asym.Rd
tcgsaseq/man/data_sim_voomlike.Rd
tcgsaseq/man/grapes-pow-grapes.Rd
tcgsaseq/man/nb_sim_fn.Rd
tcgsaseq/man/vc_test_perm.Rd
tcgsaseq/man/compute_sim_voomlike.Rd
tcgsaseq/man/deseq_fn.Rd
tcgsaseq/man/vc_score.Rd
tcgsaseq/man/nonlin_sim_fn.Rd
tcgsaseq/man/sp_weights.Rd
tcgsaseq/man/tcgsaseq.Rd
tcgsaseq/man/qAbundanceDist.Rd
tcgsaseq/LICENSE