concentration tables suitable as input for new packages?
0
0
Entering edit mode
@aa7fb9f0
Last seen 21 days ago
Germany

I would like to submit a package soon that takes as input concentration tables (csv files with one column specifiying the feature and a column specifying p.e. peak intensity/ peak area). This is normally an output of peak-processing software (such as MetaboAnalyst, Maven). When i run BiocCheck::BiocCheck() I get the warning "No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependencies. For more information, reach out to the Bioconductor community and/or consider a CRAN submission." Packages like "MetNet" use "relative abundances" of features which is comparable to "peak intensities" of metabolites. Is this input suitable for a package on Bioconductor?

Bioconductor • 333 views
ADD COMMENT
0
Entering edit mode

I'm not an expert in metabolomics but I would check out the Spectra package and other packages under the metabolomics biocviews

ADD REPLY
0
Entering edit mode

Thank you for your reply! "Spectra" indeed is another example for software processing MS-data to p.e. concentration tables. My package however does not rely on processing software but starts with concentration tables, so I would not have a dependency on other Bioconductor packages. I think that my package will be suitable to Bioconductor as it facilitates analysis of "High-throughput data" but if I run BiocCheck::BiocCheck() the warning will come up.

ADD REPLY

Login before adding your answer.

Traffic: 960 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6