gscorreia89

Hi, I have been using carveme to generate metabolic reconstructions of bacterial isolates and testing them with memote. In the "Charge Balance" test, memote is routinely flagging ~200 reactions with...

Split NMR Targeted from LC-QqQ Targeted objects

4

The features for import and QC of both targeted NMR (Bruker ivdr methods) and LC-QqQ MS assays are using the same general TargetedDataset. However, NMR Targeted methods are conceptually very...

Make tailored versions of "Feature Summary", "Feature Selection", and "Final" reports for studies without quality control samples and with repeated injections of same sample for precision calculation.

Add functionality to merge (using average/median or other features) intensity values from multiple injections of same "Sample ID" for experiments with multiple replicate injections per sample.

Currently there is functionality to calculate RSD/CV and precision measures based on SR or LTR samples. It would be interesting to make the RSD calculation functions more flexible, for example,...

Improve plotting functions - choice of color and general feature plots

1

Would be good to adapt the TIC plotting functions to: - 1) allow similar plots of individual features - 2) select metadata/parameter to color by - 3) Implement plotly interactive...

Improvements to batch correction module - specify correction sample.

2

The batch correction module should have an argument to specify which specific sample of "Precision Reference" type should be used for LOWESS correction.

There are no unitests covering parsing of Bruker ivDr BI-QUANT v2.0 files. We should: 1) Add BI-QUANT v2.0 files to the current NMR data in unitest data 2) Replicate the...

Refactor current featureMetadata fields to add improved "formal" fields for compound annotations. The goal is to allow more text description of ion and compound ids at the same time. For...