- recipe bioconductor-ptairms
Pre-processing PTR-TOF-MS Data
- Homepage
https://bioconductor.org/packages/3.14/bioc/html/ptairMS.html
- License
GPL-3
- Recipe
This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation and feature annotation. Applications to exhaled air and cell culture in headspace are described in the vignettes and examples. This package was used for data analysis of Gassin Delyle study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS), and permit to identfy four potentiel biomarquers of the infection.
- package bioconductor-ptairms¶
-
- Versions
1.2.0-1
,1.2.0-0
,1.0.0-0
- Depends
bioconductor-biobase
>=2.54.0,<2.55.0
bioconductor-msnbase
>=2.20.0,<2.21.0
bioconductor-rhdf5
>=2.38.0,<2.39.0
libblas
>=3.8.0,<4.0a0
libgcc-ng
>=10.3.0
liblapack
>=3.8.0,<4.0a0
libstdcxx-ng
>=10.3.0
r-base
>=4.1,<4.2.0a0
- Required By
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-ptairms
and update with:
conda update bioconductor-ptairms
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-ptairms:<tag>
(see bioconductor-ptairms/tags for valid values for
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-ptairms/README.html)