- recipe bioconductor-alpsnmr
Automated spectraL Processing System for NMR
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/AlpsNMR.html
- License:
MIT + file LICENSE
- Recipe:
Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.
- package bioconductor-alpsnmr¶
- versions:
4.4.0-0,4.2.0-0,4.0.0-0,3.4.0-0,3.1.5-0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-mixomics:
>=6.26.0,<6.27.0- depends r-base:
>=4.3,<4.4.0a0- depends r-baseline:
>=1.2-1- depends r-cli:
- depends r-dplyr:
>=1.1.0- depends r-fs:
>=1.2.6- depends r-future:
>=1.10.0- depends r-generics:
- depends r-ggplot2:
>=3.1.0- depends r-glue:
>=1.2.0- depends r-htmltools:
>=0.3.6- depends r-magrittr:
>=1.5- depends r-matrixstats:
>=0.54.0- depends r-pcapp:
>=1.9-73- depends r-purrr:
>=0.2.5- depends r-readxl:
>=1.1.0- depends r-reshape2:
>=1.4.3- depends r-rlang:
>=0.3.0.1- depends r-rmarkdown:
>=1.10- depends r-scales:
>=1.2.0- depends r-signal:
>=0.7-6- depends r-speaq:
>=2.4.0- depends r-stringr:
>=1.3.1- depends r-tibble:
>=1.3.4- depends r-tidyr:
>=1.0.0- depends r-tidyselect:
- depends r-vctrs:
>=0.3.0- requirements:
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-alpsnmr and update with:: mamba update bioconductor-alpsnmr
To create a new environment, run:
mamba create --name myenvname bioconductor-alpsnmr
with
myenvnamebeing 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-alpsnmr:<tag> (see `bioconductor-alpsnmr/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-alpsnmr/README.html)
