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 D, Hejblum BP (2017) Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics .


News

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

  • Fixed a bug occuring when testing several covariates together (such as several bases of time) which was giving wrong 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 for homogeneous 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

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install.packages("tcgsaseq")

1.6.2 by Boris P. Hejblum, 2 months 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]


Documentation:   PDF Manual  


GPL-2 | file LICENSE license


Imports CompQuadForm, ggplot2, GSA, KernSmooth, stats, utils

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


Suggested by TcGSA.


See at CRAN