microbiomedata metaMS issues

microbiomedata / metaMS

GC-MS Based Metabolomics Workflow

BSD 2-Clause "Simplified" License

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Add DatabaseInterface module and classes for pulling and organizing spectra from MetabRef

#58 kheal closed 1 month ago
1
Load Configuration and Calibration objects for berkeley-schema implementation

#57 kheal opened 1 month ago
0
Generate updated metadata and upload

#56 kheal opened 1 month ago
0
Modify metadata generation scripts for GC-MS Metabolomics workflow to berkeley-schema-fy24

#55 kheal opened 1 month ago
1
Merge lcms_dev into main branch of CoreMS

#54 kheal opened 2 months ago
0
Re-render documentation on lcms_dev branch on CoreMS

#53 kheal opened 2 months ago
0
Format lcms_dev branch according to PEP8 guidelines

#52 kheal opened 2 months ago
0
Add lipidomics-specific exporter to lcms_dev on CoreMS

#51 kheal closed 4 hours ago
0
Remove `to_json` method from `LCMSParameters` in `encapsulation/factory/parameters` module to `encapsulation/output/parameter_to_json` and adjust usage throughout.

#50 kheal closed 2 months ago
1
Remove api token path parameter and usage from LCMSBase object

#49 kheal closed 2 months ago
1
Modify peak picking parameters to call by relative abundance (not absolute value)

#48 kheal closed 2 months ago
1
Add functionality for parameter import/export using a tmol file

#47 kheal closed 2 months ago
1
Add private attributes and associated properties to LCMSMassFeatures class to lcms_dev on CoreMS

#46 kheal closed 1 month ago
3
Harmonize GC and LC spectral library creation and interfacing with MetabRef

#45 kheal closed 2 months ago
1
Apply properties to ChromaPeak attributes

#44 kheal closed 2 months ago
1
Develop MetabRef-specific database interface

#43 smcolby closed 3 weeks ago
0
Develop database interface base class for flexible database linking

#42 smcolby closed 3 weeks ago
0
Add lipid workflow as a test to corems

#41 kheal closed 4 hours ago
0
Add LCMS hdf5 import and export to lcms_dev on CoreMS

#40 kheal closed 1 month ago
0
Add LCMS spectra searching to lcms_dev on CoreMS

#39 kheal closed 1 day ago
0
Add LCMS peak picking functionality to lcms_dev on CoreMS

#38 kheal closed 2 months ago
0
Add LCMSMassFeature Class to chroma_peak/factory to lcms_dev on CoreMS

#37 kheal closed 2 months ago
1
Update GC-MS workflow

#36 smcolby opened 3 months ago
0
Modify GC-MS workflow to use internal standard FAMEs

#35 smcolby closed 3 weeks ago
0
Verify RT/RI calculations and test GC-MS workflow implementation to connect with Fiehn lab database

#34 smcolby opened 3 months ago
0
Modify GC-MS workflow to source MetabRef database

#33 smcolby closed 3 weeks ago
0
Add lipidomics workflow to MetaMS (cli, wdl)

#32 kheal opened 3 months ago
0
Document lipidomics workflow

#31 kheal opened 3 months ago
0
Benchmark lipidomics workflow and parameter optimization based on data in NMDC portal

#30 kheal opened 3 months ago
0
Design and enable metadata generation for lipidomics workflow

#29 kheal opened 3 months ago
2
META ISSUE: Create lipidomics workflow

#28 kheal opened 3 months ago
0
META ISSUE: Add modules and functions to CoreMS needed for lipidomics workflow

#27 kheal opened 3 months ago
1
Create in silico lipid database and load into MetabRef

#26 kheal closed 2 months ago
0
LC-MS metabolomics WDL development and Github deployment

#24 ssarrafan opened 1 year ago
11
LC-MS metabolomics CLI development

#23 ssarrafan opened 1 year ago
12
Check & confirm missing components once template and example are complete (@yuricorilo ) (September)

#22 ssarrafan closed 1 year ago
0
Generate metadata template (September)

#21 ssarrafan closed 1 year ago
0
Identify metadata components captured by DMS that are required when data is received from other institutions

#20 ssarrafan opened 1 year ago
1
MetaB-GCMS: Identify metadata components that need captured at PNNL (what isn't captured by DMS)

#19 ssarrafan closed 6 months ago
1
Collect metadata prep, QC, and Blanks / what is used at PNNL

#18 ssarrafan opened 1 year ago
1
Check & confirm missing components once template and example are complete (@yuricorilo ) (December)

#17 ssarrafan closed 1 year ago
0
Identify metadata components captured by DMS that are required when data is received from other institutions

#15 ssarrafan opened 1 year ago
0
Identify metadata components that need captured at PNNL (what isn't captured by DMS) (November)

#14 ssarrafan closed 6 months ago
0
Collect metadata for how QC and Blanks are prepped / what is used at PNNL (October)

#13 ssarrafan opened 1 year ago
0
LC-MS workflow for metabolomics data dependent analysis

#12 ssarrafan closed 1 year ago
14
Preparation Metadata: Sample Prep/Extraction

#11 mslarae13 closed 2 years ago
1
Preparation Metadata: Metabolomics

#8 mslarae13 closed 6 months ago
8
Issue with running MetaMS and minwidl

#7 Michal-Babins closed 3 years ago
4
Metabolomics pipeline prototype

#6 ssarrafan closed 1 year ago
0
Metabolomics workflow distribution outside PNNL

#5 ssarrafan closed 3 years ago
1