- recipe r-speaq
Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More detail can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.
- Homepage:
- License:
APACHE / Apache-2.0
- Recipe:
- package r-speaq¶
- Versions:
2.7.0-4,2.7.0-3,2.7.0-2,2.7.0-1,2.7.0-0,2.6.1-3,2.6.1-2,2.6.1-1,2.6.1-0,2.7.0-4,2.7.0-3,2.7.0-2,2.7.0-1,2.7.0-0,2.6.1-3,2.6.1-2,2.6.1-1,2.6.1-0,2.6.0-0,2.3.3-1,2.3.3-0,2.1.0-0,1.2.3-0,1.2.1-1,1.2.1-0- Depends:
on bioconductor-impute
on bioconductor-massspecwavelet
on r-base
>=4.5,<4.6.0a0on r-cluster
on r-data.table
on r-dosnow
on r-foreach
on r-ggplot2
on r-gridextra
on r-missforest
on r-reshape2
on r-rfast
on r-rvest
on r-xml2
- 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 r-speaq
to add into an existing workspace instead, run:
pixi add r-speaq
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 r-speaq
Alternatively, to install into a new environment, run:
conda create -n envname r-speaq
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/r-speaq:<tag>
(see r-speaq/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/r-speaq/README.html)
