Minghao Gong

Perform peak detection with a defined roilist

4

Hi Johannes, Have been going through several options to perform peak detection with a defined list of ROI. I accidentally used `ManualChromPeak` and at the end found out that there...

plot log2-transformed intensity in XIC

7

Hi Johannes, Is there a way I can plot the log2-transformed intensities instead of absolute intensities? The intensities of some peaks are too dramatic and they masked my important small...

subset retention time alignment

2

Dear XCMS community: I got the following errors when doing retention time alignment based on peak group alignment on "subset"

Export region of interest?

3

Dear XCMS developer, A quick question for you: where can I find the function to export the list of regions of interest? Thanks, Minghao Gong

Reactions that have good blast but not included in the draft model

1

Dear Gapseq developer, I am super excited about this software. It does improve CarveMe and ModelSeed draft models a lot and it provides a long list of tentative reactions, which...

Hi Hideto Mori, Is there a way to outline the text on the circle like the image below?  Thanks, Minghao Gong

Identification of outlier samples in plotAdjustedRtime plot

9

Hi Johannes, Thanks very much for the continuous supports in this github. I would like to ask if there is a easy way to figure out which is the outlier...

Dear developers, > Importantly, the weights of the features within a view have relative values and they should not be interpreted in an absolute scale. Therefore, for interpretability purposes we...

Tuple in the config dictionary changed to string when run a python notebook with papermill

1

## 🐛 Tuple in the config dictionary changed to string when run a python notebook with papermill I used the current config to run papermill with the following script ####...

precursorMz of hmdb Spectra object are NAs

5

Hi Johannes, I just realized that precursorMz is another important check on the matched spectra between samples and database. Only if both precursorMz matched should the spectra comparison meaningful. I...