replicate 1
passAnswer
5.81798037353593
Workflow
UDT: codex-pydeseq2-gseapy-reactome-p53-or
Question
What is the odds ratio for p53-mediated cell cycle gene regulation in an enrichment analysis using gseapy with Reactome_2022 using all statistically differentially expressed genes from a pydeseq2 analysis that includes all related treatment groups (DMSO, DMSO_Serum_starvation, Cisplatin_IC50_CBD_IC50, Cisplatin_IC50_CBD_IC50_Serum_starvation_16h) for proper dispersion estimation, after pre-filtering to keep only genes with counts greater than 10 in at least one of all 30 samples, (padj<=0.05, absolute lfc>=0.5, baseMean>=10) between CBD/cisplatin combination treatment and DMSO?
Galaxy-API code with skills
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passAnswer
5.81798037353593
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UDT: codex-pydeseq2-gseapy-reactome-or2UDT: codex-pydeseq2-gseapy-reactome-or3UDT: codex-pydeseq2-gseapy-reactome-or4
replicate 3
failAnswer
4.691674580563469
Workflow
UDT: codex-pydeseq2-combo-dmso-foregroundgseapy enrichr
Galaxy-API code without skills
3/3 passreplicate 1
passAnswer
5.812405901836796
Workflow
UDT: codex_pydeseq2_gseapy_reactome_p53_v1
replicate 2
passAnswer
5.812405901836796
Workflow
pydeseq2-cbd-cisplatin-dmso-20260708102158gseapy enrichr
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passAnswer
5.812405901836796
Workflow
UDT: codex_pydeseq2_gseapy_reactome_p53_or_v1
Open-ended code with skills
0/3 passreplicate 1
failAnswer
5.840347891851011
Workflow
local codePyDESeq2GSEApyEnrichrReactome
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failAnswer
6.12816088009491
Workflow
local codePyDESeq2GSEApyEnrichrReactome
replicate 3
failAnswer
5.84034789185101
Workflow
local codePyDESeq2GSEApyEnrichrReactome
Open-ended code without skills
0/3 passreplicate 1
failAnswer
5.840347891851011
Workflow
local codePyDESeq2GSEApyReactome
replicate 2
failAnswer
5.840347891851011
Workflow
local codePyDESeq2GSEApyReactome
replicate 3
failAnswer
5.840347891851011
Workflow
local codePyDESeq2GSEApyReactome