- recipe bioconductor-topconfects
Top Confident Effect Sizes
LGPL-2.1 | file LICENSE
Rank results by confident effect sizes, while maintaining False Discovery Rate and False Coverage-statement Rate control. Topconfects is an alternative presentation of TREAT results with improved usability, eliminating p-values and instead providing confidence bounds. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change, but it can be applied to any collection of effect sizes with associated standard errors.
- package bioconductor-topconfects¶
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-topconfects and update with:: mamba update bioconductor-topconfects
To create a new environment, run:
mamba create --name myenvname bioconductor-topconfects
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-topconfects:<tag> (see `bioconductor-topconfects/tags`_ for valid values for ``<tag>``)