CoGAPS
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FertigLab
Bayesian MCMC matrix factorization algorithm
Good afternoon, Thank you so much for the detailed vignettes and papers for using CoGAPS. We are really finding it beneficial to our research. We are running CoGAPS using the...
hello! I am trying to run gene enrichment and I can't find the argument in calcCoGAPSStat that would accept a gene list. Any advice would be appreciated! Here is the...
Hello I ran the vignette but I have some troubles on interpreting the results. 1. The rows in the example matrix have a prefix _Hs._ followed by a number. Is...
I'm using scCoGAPS and haven't been able to use the checkpoint saving steps. I found that the `checkpointsEnabled()` is set to `FALSE`, with no clear way to change this. I've...
According to the most recent vignettes (found https://www.bioconductor.org/packages/devel/bioc/vignettes/CoGAPS/inst/doc/CoGAPS.html and https://bioconductor.org/packages/release/bioc/vignettes/CoGAPS/inst/doc/CoGAPS.html) CoGAPS 3.8 and 3.9 should be the most recent versions. However, when I install from Github, 3.7 is the version...
Exported methods getAmplitudeMatrix and getPatternMatrix
Exported getAmplitudeMatrix and getPatternMatrix functions
Thanks for this wonderful work. I tried to learn the pattern from dataset A then transfer to dataset B for annotation, but I am a bit confused about how to...
When sampling with annotated weights to make subsets, the final CoGAPS results has repeated samples in the Sample Factor Matrix. Should the sample weights be averaged by sample for each...
Apologies for breaking your package by changing the returned value of Rhdf5lib::pkg_config(). It looks like you've removed the dependency on this, and based on a cursory look can't see where...
