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tcgsaseq

Time-Course Gene Set Analysis for RNA-Seq Data

Analyze RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights. Perform both gene-wise and gene set analyses, and can deal with longitudinal data. Method is detailed in: Agniel & Hejblum (2017) , Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604.

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Overview

tcgsaseq is a package for analyzing RNA-seq data. The 2 main functions of the package are varseq and tcgsa_seq:

  • Gene-wise Differential Analysis of RNA-seq data can be performed using the function varseq.
  • Gene Set Analysis of RNA-seq data can be performed using the function tcgsa_seq.

The method implemented in this package is detailed in the following article:

Installation

The easiest way to get tcgsaseq is to install it from CRAN:

install.packages("tcgsaseq")

Or to get the development version from GitHub:

devtools::install_github("denisagniel/tcgsaseq")

-- Denis Agniel and Boris Hejblum

News

News about the tcgsaseq R package

Main changes in Version 1.8.1 (2018-12-06):

  • perm_pe function for exact p-values and accurate FDR control when using permutation test. The column names of the $pvals output are back to being the same regardless of the test chosen being asympotic or permutation
  • dsFDR is not used anymore

Main changes in Version 1.8.0 (2018-11-23):

  • dsFDR function for accurate discrete FDR control when using permutation test. This changes the column names of the $pvals output when which_test = permutations

Main changes in Version 1.7.2 (2018-07-18):

  • faster permutations

Main changes in Version 1.7.1 (2018-07-07):

  • faster implementation

Main changes in Version 1.6.5 (2017-12-24) --- this is only a minor release:

  • bug fix in the log2-cpm transformation computation (for preprocessed = FALSE) in sp_weights
  • bug fix in sp_weights when facing NA or NaNvalues

Main changes in Version 1.6.3 (2017-11-09)

  • WARNING instead of ERROR when a gene set with no measured genes is tested
  • NA support through na.rm_... logical arguments
  • bug fix for row.names error in weights computation for gene-wise analysis

Main changes in Version 1.6.2 (2017-08-04)

  • bug fix to the log2-cpm transformation computation (for preprocessed = FALSE)
  • improvement to defaults in varseq and tcgsa_seq wrapper functions, including an option to compute heteroscedasticity weights without conditioning on the variable(s) to be tested

Main changes in Version 1.5.2 (2017-07-11)

  • user-friendly wrapper function varseq for gene-wise testing
  • RAM usage optimization

Main changes in Version 1.5.1 (2017-05-24) --- this is only a minor release:

  • homogeneous test now available for gene-wise testing.

Main changes in Version 1.5.0 (2017-03-27):

  • permutation test now available for gene-wise testing

Main changes in Version 1.4.0 (2017-02-21):

  • bug fix for gene-wise testing

Main changes in Version 1.3.1 (2016-11-24):

  • bug fix for testing several covariates together (such as several bases of time) which now gives correct p-values
  • support for gene-wise testing
  • example dataset 'baduel_small' was changed to 'baduel_5gs' which includes 1943 additional gene expressions and the definition of 5 gene sets
  • documentation updated

Main changes in Version 1.2.0 (2016-07-19):

  • support homogeneous gene set test
  • documentation updated

Main changes in Version 1.1.0 (2016-05-26):

  • improved imports
  • documentation updated

Main changes in Version 1.0.2 (2016-05-18) --- this is only a minor release:

  • documentation and CITATION updated

Main changes in Version 1.0.1 (2016-05-14) --- this is only a minor release:

  • help file improvements

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.
install.packages("tcgsaseq")

2.0.5 by Boris P. Hejblum, a month ago

Report a bug at https://github.com/denisagniel/tcgsaseq/issues

Browse source code at https://github.com/cran/tcgsaseq

Authors: Denis Agniel [aut] , Boris P. Hejblum [aut, cre] , Marine Gauthier [aut]

Documentation:   PDF Manual  

GPL-2 | file LICENSE license

Imports CompQuadForm, ggplot2, graphics, GSA, KernSmooth, parallel, pbapply, stats, statmod, utils

Suggests limma, edgeR, DESeq2, S4Vectors, knitr, rmarkdown, testthat, covr

Suggested by TcGSA.

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