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metaMS
GC-MS Based Metabolomics Workflow
BSD 2-Clause "Simplified" License
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Add CI/CD to test wdl validity
#60
kheal
closed
1 month ago
1
Upgrade wdl to version 1.0
#59
kheal
closed
1 month ago
1
Add DatabaseInterface module and classes for pulling and organizing spectra from MetabRef
#58
kheal
closed
3 months ago
1
Load Configuration and Calibration objects for berkeley-schema implementation
#57
kheal
closed
1 month ago
1
Generate updated metadata and upload
#56
kheal
closed
1 month ago
1
Modify metadata generation scripts for GC-MS Metabolomics workflow to berkeley-schema-fy24
#55
kheal
closed
1 month ago
2
Merge lcms_dev into main branch of CoreMS
#54
kheal
opened
4 months ago
0
Re-render documentation on lcms_dev branch on CoreMS
#53
kheal
opened
4 months ago
0
Format lcms_dev branch according to PEP8 guidelines
#52
kheal
opened
4 months ago
0
Add lipidomics-specific exporter to lcms_dev on CoreMS
#51
kheal
closed
1 month 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
4 months ago
1
Remove api token path parameter and usage from LCMSBase object
#49
kheal
closed
4 months ago
1
Modify peak picking parameters to call by relative abundance (not absolute value)
#48
kheal
closed
4 months ago
1
Add functionality for parameter import/export using a tmol file
#47
kheal
closed
4 months ago
1
Add private attributes and associated properties to LCMSMassFeatures class to lcms_dev on CoreMS
#46
kheal
closed
3 months ago
3
Harmonize GC and LC spectral library creation and interfacing with MetabRef
#45
kheal
closed
4 months ago
1
Apply properties to ChromaPeak attributes
#44
kheal
closed
4 months ago
1
Develop MetabRef-specific database interface
#43
smcolby
closed
2 months ago
0
Develop database interface base class for flexible database linking
#42
smcolby
closed
2 months ago
0
Add lipid workflow as a test to corems
#41
kheal
closed
1 month ago
0
Add LCMS hdf5 import and export to lcms_dev on CoreMS
#40
kheal
closed
3 months ago
0
Add LCMS spectra searching to lcms_dev on CoreMS
#39
kheal
closed
2 months ago
0
Add LCMS peak picking functionality to lcms_dev on CoreMS
#38
kheal
closed
4 months ago
0
Add LCMSMassFeature Class to chroma_peak/factory to lcms_dev on CoreMS
#37
kheal
closed
4 months ago
1
Update GC-MS workflow
#36
smcolby
opened
5 months ago
0
Modify GC-MS workflow to use internal standard FAMEs
#35
smcolby
closed
2 months ago
0
Verify RT/RI calculations and test GC-MS workflow implementation to connect with Fiehn lab database
#34
smcolby
closed
1 month ago
1
Modify GC-MS workflow to source MetabRef database
#33
smcolby
closed
2 months ago
0
Add lipidomics workflow to MetaMS (cli, wdl)
#32
kheal
opened
5 months ago
0
Document lipidomics workflow
#31
kheal
opened
5 months ago
0
Benchmark lipidomics workflow and parameter optimization based on data in NMDC portal
#30
kheal
opened
5 months ago
0
Design and enable metadata generation for lipidomics workflow
#29
kheal
opened
5 months ago
4
META ISSUE: Create lipidomics workflow
#28
kheal
opened
5 months ago
0
META ISSUE: Add modules and functions to CoreMS needed for lipidomics workflow
#27
kheal
opened
5 months ago
1
Create in silico lipid database and load into MetabRef
#26
kheal
closed
4 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
2 years ago
1
MetaB-GCMS: Identify metadata components that need captured at PNNL (what isn't captured by DMS)
#19
ssarrafan
closed
8 months ago
1
Collect metadata prep, QC, and Blanks / what is used at PNNL
#18
ssarrafan
opened
2 years 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
2 years ago
0
Identify metadata components that need captured at PNNL (what isn't captured by DMS) (November)
#14
ssarrafan
closed
8 months ago
0
Collect metadata for how QC and Blanks are prepped / what is used at PNNL (October)
#13
ssarrafan
opened
2 years 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
8 months ago
8
Issue with running MetaMS and minwidl
#7
Michal-Babins
closed
3 years ago
4
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