recipe bioconductor-pepsettest

Peptide Set Test

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/PepSetTest.html

License:

GPL (>= 3)

Recipe:

/bioconductor-pepsettest/meta.yaml

Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights.

package bioconductor-pepsettest

(downloads) docker_bioconductor-pepsettest

versions:

1.0.0-0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-lme4:

depends r-mass:

depends r-matrixstats:

depends r-reshape2:

depends r-tibble:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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-pepsettest

and update with::

   mamba update bioconductor-pepsettest

To create a new environment, run:

mamba create --name myenvname bioconductor-pepsettest

with myenvname being 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-pepsettest:<tag>

(see `bioconductor-pepsettest/tags`_ for valid values for ``<tag>``)

Download stats