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Add TOC bullot for BP, MF, CC

master . 7dcc75...c8b04f . push triggered

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More comments

master . b6148a...7dcc75 . push triggered

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fmt

master . a49318...b6148a . push triggered

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fmt

master . 717236...a49318 . push triggered

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Add documentation regarding BP, MF, CC

master . 040b4d...717236 . push triggered

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Now using GOEnrichmentStudyNS, rather than GOEnrichmentStudy, to run separate GO...

master . 7d90f1...040b4d . push triggered

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GoeaResults not needed

master . 9410da...7d90f1 . push triggered

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Apply multiple test correction within each of the 3 major GO categories.

master . 633b09...9410da . push triggered

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Add -ev_help_short

master . 310f3c...633b09 . push triggered

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Move print functions to their own class so they may be used by multiple classes

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Add ns2assc for: GPAD, GAF, NCBI's gene2go, original id2gos annotation formats.

master . 407682...f55230 . push triggered

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Add annotation init package

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Add NS field to GPAD and id2gos if godag is provided

master . c840d1...695071 . push triggered

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Add code to include/exclude annotations by evidence code.

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Evidence code details

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Evidence code examples

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Evidence code help

master . 6ca91f...f33433 . push triggered

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Add evidence code print help

master . c388a5...6ca91f . push triggered

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Begin to document include/exclude evidence codes

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Prep for controlling which evidence codes are used across all formats: GPAD GAF...

master . fbc62e...bc30f4 . push triggered

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