shuzhao-li-lab PythonCentricPipelineForMetabolomics issues

shuzhao-li-lab / PythonCentricPipelineForMetabolomics

Python pipeline for metabolomics data preprocessing, QC, standardization and annotation

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Difference between pre-annotation and level 4 annotaion in pcpfm

#81 pickyseok opened 5 hours ago
0
WSL

#80 jmmitc06 opened 2 days ago
0
can you provide an example file for sequence.csv ?

#79 pickyseok closed 3 days ago
3
Slidev for figures

#78 jmmitc06 opened 1 month ago
0
Add CV plots to output

#77 jmmitc06 opened 1 month ago
0
Pcpfm output - annotation_table.tsv don't have feature's original m/z and adduct type assignment in the column

#76 gmhhope closed 1 month ago
5
ThermoRawFileConverter does not work on GC Data

#75 jmmitc06 closed 3 months ago
4
multi-core processing for map_ms2

#74 YasinEl opened 4 months ago
1
asari cannot locate mzml files from assebled experiment

#73 YasinEl closed 1 month ago
7
scipy dependency in matchms

#72 shuzhao-li closed 4 months ago
1
Support all mQACC best practices during data processing.

#71 jmmitc06 opened 5 months ago
0
Mass differences for EI-MS variant of Khipu

#70 jmmitc06 opened 5 months ago
0
Mirror Plots for EI-MS / MS2

#69 jmmitc06 opened 5 months ago
0
Reset command example

#68 gmhhope closed 6 months ago
2
TOC for Report

#67 jmmitc06 opened 6 months ago
0
Cross-device link" error when running assemble

#66 gmhhope opened 7 months ago
2
Replace __extract__

#65 jmmitc06 closed 7 months ago
1
Enforce collision energy matching for MS2

#64 jmmitc06 opened 8 months ago
0
controlled vocabulary restriction for feature tables / empcpds

#63 jmmitc06 closed 4 months ago
2
Better description of PDF contents

#62 jmmitc06 closed 7 months ago
1
More detailed descriptions of the inputs and outputs

#61 jmmitc06 closed 1 month ago
1
DDA scan should be togglable

#60 jmmitc06 closed 8 months ago
1
Correlation heatmap tick marks

#59 jmmitc06 opened 8 months ago
0
Singletons are not annotated using L4 annotation methods.

#58 jmmitc06 closed 8 months ago
1
Anaconda version

#57 jmmitc06 closed 4 months ago
1
Start analysis without metadata

#56 jmmitc06 opened 9 months ago
0
Start analysis with exsiting table

#55 jmmitc06 opened 9 months ago
0
Better inferencing of missing metadata fields.

#54 jmmitc06 closed 4 months ago
5
Issue with figure generation when called multiple times

#53 jmmitc06 closed 9 months ago
1
Sequence file with empty field or nan won't be handle properly in JSON file.

#52 gmhhope closed 9 months ago
11
metadata field for a quick look at the group/class... during pcpfm run

#51 gmhhope closed 9 months ago
3
Signaling completion for each step while running the command lines

#50 gmhhope closed 9 months ago
2
Run through but w/t errors that want to be clarified.

#49 gmhhope closed 8 months ago
30
Enhanced Organization and Utility of Example Scripts

#48 gmhhope closed 9 months ago
7
A central place (JSON file?) to provide comprehensive Field Mapping Guidelines for User-friendly understanding of the implied rule.

#47 gmhhope closed 9 months ago
3
Harmonize output metadata

#46 jmmitc06 opened 9 months ago
0
Log transformation issue

#45 jmmitc06 closed 9 months ago
1
Replace Pycombat

#44 jmmitc06 closed 1 month ago
1
Add support for special metadata types

#43 jmmitc06 closed 7 months ago
2
Avoid "example" files under pcpfm

#42 shuzhao-li closed 9 months ago
1
Unit testing / Validation testing

#41 jmmitc06 opened 1 year ago
0
Align annotations results with metdata model.

#40 jmmitc06 closed 10 months ago
1
Maybe we can introduce more about example bash scripts

#39 YuanyeChi closed 11 months ago
2
Non-MSP file formats for Annotate

#38 jmmitc06 closed 1 year ago
1
Support for multiple MSP annotation source

#37 jmmitc06 closed 1 year ago
1
Add region support for manual integration

#36 jmmitc06 opened 1 year ago
0
Metadata support for non-orbis

#35 jmmitc06 closed 1 month ago
1
Support raw file formats directly

#34 jmmitc06 opened 1 year ago
0
QA/QC Figures for Rejected Samples

#33 jmmitc06 opened 1 year ago
0
Put on Anaconda

#32 jmmitc06 closed 1 month ago
1