recipe bioconductor-msstatslobd

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MSstatsLOBD.html

License:

Artistic-2.0

Recipe:

/bioconductor-msstatslobd/meta.yaml

The MSstatsLOBD package allows calculation and visualization of limit of blac (LOB) and limit of detection (LOD). We define the LOB as the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured. The LOD is defined as the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence. These functionalities were previously a part of the MSstats package. The methodology is described in Galitzine (2018) <doi:10.1074/mcp.RA117.000322>.

package bioconductor-msstatslobd

versions:

1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-2,  1.6.0-1,  1.6.0-0,  1.2.0-2,  1.2.0-1,  1.2.0-0, 

1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-2,  1.6.0-1,  1.6.0-0,  1.2.0-2,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

depends r-minpack.lm:

depends r-rcpp:

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-msstatslobd

and update with::

   mamba update bioconductor-msstatslobd

To create a new environment, run:

mamba create --name myenvname bioconductor-msstatslobd

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-msstatslobd:<tag>

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

Download stats

Link to this page

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