Pipeline: tagged counting repurposed as classifier#241

Merged

taimontgomery merged 18 commits intomasterfrom

Oct 27, 2022

Commits on Oct 16, 2022

Changing the internal and external names of the Tag column
AlexTate
committed
First draft changes in tiny-count
AlexTate
committed
tiny-deseq.r has been updated to handle feature counts using the new table format. The Feature Class column has been dropped and the Tag column has been renamed to Classifier.
AlexTate
committed

Commits on Oct 18, 2022

class_charts and scatter_by_dge_class have been updated to treat the Tag multiindex column as a classifier. Wow, this opened the door for some really satisfying simplifications to the class-related…
AlexTate
committed
Renaming the "tags" attribute in the Features class to "classes" for consistency.
AlexTate
committed
Adding two new command line options to tiny-plot:
AlexTate
committed
Including new parameters for labelling unknown/unassigned classes
AlexTate
committed
Updated the Features Sheet example for the new column configuration
AlexTate
committed
Description of class counting via the Class= attribute has been removed from the file requirements table.
AlexTate
committed
The Tagged Counting section has been rewritten to describe the new "classified" counting approach.
AlexTate
committed
Removed references to Class= counting in the class_charts description. The count normalization section has been removed because it no longer applies with the new counting method. A link to the corr…
AlexTate
committed
Adding new parameters for unassigned/unknown class labels to the CWL and Run Configs
AlexTate
committed
Updating column config in the features.csv template
AlexTate
committed
Added a brief check in the CSV reader to catch usage of Features Sheets with a Tag column. Previously, the user would have been notified that the "Classify as..." column was missing from their Feat…
AlexTate
committed
Merge branch 'master' into issue-240
AlexTate
committed

Commits on Oct 22, 2022