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Human 1.16 #645
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Human 1.16 #645
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- GEO: GSE75189
…ctions feat: enable `sanityCheck.py` to check unused mets and genes
Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>
fix: fatal importYaml bug
Fix Representation of ETF
Fix Reactions Related To CLYBL
fix: add GPRs and references for MAR09985 and MAR11307
- The changes in this commit are to move subsystem reading code into the "case" of reading confidence_score. This optimise the logic of loading subSystems according the Yaml file structure.
… MAR20015 into row for MAR04689, then remove MAR20015
…hen remove MAR20014
…hen remove MAR20052
- This commit includes fixing typos, and reverting back to original way of extracting subsystem values
fix-add a error report in the import/export cycle
…GPR_rxns Fix/merge same stoich same gpr rxns
feiranl
approved these changes
Jun 18, 2023
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LGTM!
- cherry pick `adjust_pvalues` function from repo GeneSetAnalysisMatlab for convenient use
…itySuite feat: add hart2015 essentiality suite
now the Hart2015 essentiality suite (#563) is added to this release, with following results:
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Main improvements in this PR:
MAR20015
,MAR20014
,MAR20052
for being duplicates ofMAR04689
,MAR06981
,MAR00067
, repectively, based on Suspected duplicated reactions #630, as suggested in GPRs for MAR09985 and MAR11307 #588:
Fixes (PR Fix Representation of ETF #612)
MAM02443c
,MAM02443m
,MAM02443r
, andMAM02443x
to "malonyl-carnitine"MAM02443e
MAM03494c
andMAM03494e
withMAM02443c
andMAM02443e
inMAR04886
andMAR11256
MAR05434
for being redundant withMAR02599
MAM03494c
andMAM03494e
for being redundant withMAM02443c
andMAM02443e
MAM03494c/e
into current annotations forMAM02443c/e
in metabolites.tsvENSG00000172331
toENSG00000119640 or ENSG00000170634
, as discussed in Inaccurate GPR of MAR04372 #587MAR05295
,MAR06894
, andMAR06895
ENSG00000140675
fromMAR05029
MAR05429
toMAR05295
MAR01444
toATP [c] + H2O [c] + K+ [e] + H+ [e] + 2 Na+ [c] ⇒ ADP [c] + Pi [c] + K+ [c] + H+ [c] + 2 Na+ [e]
, GPR:ENSG00000075673 and ENSG00000186009
sanityCheck.py
to check unused mets and genes #556)sanityCheck.py
by enabling detection of unused metabolites, triggered by mistakes found in fix: refine reactions, reversibility, and GPRs of Isocitrate Dehydrogenase metabolism #525