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Synthetic data benchmarking pipeline#8

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ctrlaltaf wants to merge 29 commits intoReed-CompBio:mainReed-CompBio/spras-benchmarking:mainfrom ctrlaltaf:pipelinectrlaltaf/spras-benchmarking:pipelineCopy head branch name to clipboard

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Commits on Oct 29, 2024

• added preprocessing files

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  2b034cc

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Commits on Oct 30, 2024

• added initial namespace files

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  38add56

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• updated mapper

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• updated docs

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Commits on Nov 4, 2024

• initial snakemake workflow

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  8dd5fb2

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• setup figure generation

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  1e4c523

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Commits on Nov 5, 2024

• added stats calculation

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• added edge overlap stats

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• added scores stats

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• added auc images

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  935d19b

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• refactoring

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• refactored code

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• updated structure to take algorithm and pathway combo

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• initial structure for algorithm auc

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  e4a9843

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• cleaned up code

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  56ebd9d

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• combined auc for algorithm and pathway category

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  23ee963

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• cleaned up code

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  6c53479

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Commits on Nov 6, 2024

• refactored outputs

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  d40371b

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• added heatmap

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  6197b92

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• added heatmap

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  a0c39dd

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• added new sample dataset

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  5e65ab5

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• updated config

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Commits on Nov 7, 2024

• refactoring

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  69833a4

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Commits on Nov 8, 2024

• modularized heatmap w/ algorithm pathway combo

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  8373ceb

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• updated config and cleaned up code

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  8b399e4

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• refactored heatmap

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  b3aa213

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• removed obsolete files

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  a578c0b

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Commits on Nov 11, 2024

• updated documentaion

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  f5571b4

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Commits on Feb 14, 2025

• testing

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