tetomonti

Anthony, I created a 'dev' branch and edited the `ks_enrichment.R` file to add "leading edge" functionalities. In particular, * the `.ks_test` function now returns two extra parameters: `leading_edge` and `leading_hits`,...

Thank you, it worked! Perhaps worth updating the Bioconductor page: searching for TCGAbiolinks sends you here: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html Thanks > On Sep 19, 2022, at 11:09 PM, Tiago Chedraoui Silva ***@***.***>...

Eventually, if possible, the caching should work as follows: * if the requested `n_perm` is _larger_ than the cached value, then the permutations need to be run (i.e., the cached...

Actually, I think it would be more appropriate when running the permutation testing.

Most important is at permutation level (i.e., cadra_search). Need to turn it off at inner level (i.e., topn_eval or candidate_search) if called from cadra_search. see `plyr::alply( ..., .progress =...)` for...

Looks like you ( @RC-88 ) are probably working on this, that's great! Please notice that when running it, there is a lot of messaging and other output (e.g., the...

Move/Copy the github.io [vignette](https://montilab.github.io/CaDrA/articles/docs/yaptaz_example.html) to `README.rmd`

Hi Vinay, glad you’re testing it. Please, let us know if you see anything else worth addressing Re your question, if you want the increased ranking (rather than decreasing), couldn’t...

Yes, it reorders based on sort, but sort(input_score) and sort(-input_score) will be opposite, so you can input one or the other depending on what you want. Or am I misunderstanding...

CaDrA is supposed to work w/ scoring functions other than rank-based, e.g., Mutual Information or Correlation, in which case the actual input score is needed, not simply the ranking of...