- recipe bioconductor-dearseq
Differential Expression Analysis for RNA-seq data through a robust variance component test
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/dearseq.html
- License:
GPL-2 | file LICENSE
- Recipe:
Differential Expression Analysis 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 repeated or longitudinal data. Methods are detailed in: i) Agniel D & Hejblum BP (2017) Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604 ; and ii) Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2020) dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, NAR Genomics and Bioinformatics, 2(4):lqaa093.
- package bioconductor-dearseq¶
- Versions:
1.22.0-0,1.18.0-0,1.14.0-0,1.12.1-0,1.10.0-0,1.6.0-0,1.4.0-0,1.2.0-1,1.2.0-0,1.22.0-0,1.18.0-0,1.14.0-0,1.12.1-0,1.10.0-0,1.6.0-0,1.4.0-0,1.2.0-1,1.2.0-0,1.0.0-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-compquadform
on r-dplyr
on r-ggplot2
on r-kernsmooth
on r-magrittr
on r-matrixstats
on r-patchwork
on r-pbapply
on r-reshape2
on r-rlang
on r-scattermore
on r-statmod
on r-survey
on r-tibble
on r-viridislite
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install bioconductor-dearseq
to add into an existing workspace instead, run:
pixi add bioconductor-dearseq
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install bioconductor-dearseq
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-dearseq
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/bioconductor-dearseq:<tag>
(see bioconductor-dearseq/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-dearseq/README.html)
