Clean up Roxygen parametrs and descriptions#84

Merged

phoman14 merged 45 commits intoDEVfrom

Mar 26, 2026

Commits on Mar 23, 2026

Commits on Mar 24, 2026

fixed typo param mad.topNgenes.limitsSet
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Merge branch 'DEV_PhilSprint' of github.com:NIDAP-Community/SCWorkflow into DEV_PhilSprint
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Update Test for FilterQC
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clean up vignette quotation ussaage
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Merge branch 'DEV_PhilSprint' of https://github.com/NIDAP-Community/SCWorkflow into DEV_PhilSprint
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Modscore change to standard output
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colorByMarkerTable-clean up function parameter layout and coment out library load
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fix Samples Bug in Plot_Metadata
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plot Metadata rearange function parameters
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Merge branch 'DEV_PhilSprint' of github.com:NIDAP-Community/SCWorkflow into DEV_PhilSprint
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Plot Metadata test error plot->plots for output
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Standardize parameters so that _->. and fix typo in parameter
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standardize parameters for inst/shiny/ModuleScoreApp
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modify test to look for plots instead of plot
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colorByGene-resolved cant find Samples error
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Merge branch 'DEV_PhilSprint' of https://github.com/NIDAP-Community/SCWorkflow into DEV_PhilSprint
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minor error fixes to test files to run correctly
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remove explicetly loading library in function
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return standard output list data and plot
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removue redundant use of samples to us only samples.to.include
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Harmony make standard object list of object and plots
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Harmony remove uncessary print statements
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Add title and description from .json files for Annotate_Cell_Types.R, DEG_Gene_Expression_Markers.R,Dual_Labeling.R,Filter_QC.R,Filter_Seurat_Object_by_Metadata.R
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add example function calls to roxygen section. Standardize Roxygen format between all functions
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