- recipe bioconductor-isocorrector
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/IsoCorrectoR.html
- License:
GPL-3
- Recipe:
IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O…), as well as ultra-high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously). See the Bioconductor package IsoCorrectoRGUI for a graphical user interface to IsoCorrectoR. NOTE: With R version 4.0.0, writing correction results to Excel files may currently not work on Windows. However, writing results to csv works as before.
- package bioconductor-isocorrector¶
- Versions:
1.28.0-0,1.24.0-0,1.20.0-0,1.18.0-0,1.16.0-0,1.12.0-0,1.10.0-0,1.8.0-1,1.8.0-0,1.28.0-0,1.24.0-0,1.20.0-0,1.18.0-0,1.16.0-0,1.12.0-0,1.10.0-0,1.8.0-1,1.8.0-0,1.6.0-0,1.4.0-0,1.2.1-0,1.2.0-0,1.0.5-0- Depends:
on r-base
>=4.5,<4.6.0a0on r-dplyr
on r-magrittr
on r-pracma
on r-quadprog
on r-readr
on r-readxl
on r-stringr
on r-tibble
on r-writexls
- 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-isocorrector
to add into an existing workspace instead, run:
pixi add bioconductor-isocorrector
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-isocorrector
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-isocorrector
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-isocorrector:<tag>
(see bioconductor-isocorrector/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-isocorrector/README.html)
