- recipe bioconductor-qvalue
Q-value estimation for false discovery rate control
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/qvalue.html
- License:
LGPL
- Recipe:
This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.
- package bioconductor-qvalue¶
- Versions:
2.42.0-0,2.38.0-0,2.34.0-0,2.32.0-0,2.30.0-0,2.26.0-0,2.24.0-0,2.22.0-1,2.22.0-0,2.42.0-0,2.38.0-0,2.34.0-0,2.32.0-0,2.30.0-0,2.26.0-0,2.24.0-0,2.22.0-1,2.22.0-0,2.20.0-0,2.18.0-1,2.18.0-0,2.16.0-1,2.16.0-0,2.14.1-0,2.14.0-0,2.12.0-0,2.10.0-0,2.8.0-0,2.6.0-0,2.4.2-0,2.2.2-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-ggplot2
on r-reshape2
- 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-qvalue
to add into an existing workspace instead, run:
pixi add bioconductor-qvalue
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-qvalue
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-qvalue
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-qvalue:<tag>
(see bioconductor-qvalue/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-qvalue/README.html)
