recipe ionquant

A label free quantification tool

Homepage:

https://github.com/Nesvilab/IonQuant

License:

Academic License (https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf)

Recipe:

/ionquant/meta.yaml

Links:

biotools: fragpipe, doi: 10.1074/mcp.TIR120.002048

IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies.

IonQuant is available freely for academic research and educational purposes only, in accordance with the terms at https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf.

package ionquant

(downloads) docker_ionquant

versions:

1.10.12-1,  1.10.12-0

depends openjdk:

>=11

depends python:

>=3.8

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 ionquant

and update with::

   mamba update ionquant

To create a new environment, run:

mamba create --name myenvname ionquant

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/ionquant:<tag>

(see `ionquant/tags`_ for valid values for ``<tag>``)

Notes

The "ionquant" command runs the IonQuant java program.

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