CoGAPS
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FertigLab
Bayesian MCMC matrix factorization algorithm
- add a test that fails on empty patterMarkers - make it pass by rewriting the method for threshold='all'
Related to #102. It is not explicitly defined how the patternMarkers() threshold needs to operate, this function needs to be refactored. - document modes (thresholds) - document and review simplicityGENES()...
The codebase for CoGAPS has become hard to navigate as more and more functionality was added with time. Let's add comments to the most essential and hard to understand parts...
Hi! I am trying to obtain patternMarkers from a cogaps result object using the following code: pMarks
Can we get saving and starting from Checkpoints reinitialized for CoGAPS? Otherwise given the execution speed the results are lost if runtime is longer than the time limit for some...
There used to be a semi-supervised [CoGAPS version](https://github.com/FertigLab/CoGAPS-bioc/blob/master/R/gapsMapRun.R) that seem to have disappeared. ##Can it be brought back? - [ ] create a plan - [ ] https://github.com/FertigLab/CoGAPS/issues/76 ##And make...
I am running `CoGAPS` on a small single-cell data set: 11623 genes x 900 cells. I have noticed that when I run `CoGAPS` in distributed mode, it will not produce...
it has been reported that the default number of patters is suboptimal and confusing. Is there a way to set it in a smarter way than simply choosing 7 ([currently...
Hi, I have two data sets I wish to cross compare, but instead of learning N patterns from an experiment what I would like is to set the pattens manually...
