Jean Fan

They should be automatically loaded. Based on the error you saw previously: ``` models: Error: 'bplapply' receive data failed: error reading from connection ``` it sounds like this could be...

Dear Joanne, Thanks for trying out HoneyBADGER. It looks like there may be some issues with using the S4 object class. Can you please try running HoneyBADGER without using the...

Dear Joanne, Without seeing the error, it is difficult for me to speculate on what may be happening here. But to walk you through the code: results

Dear Teng, Thanks for sharing your output and the well organized issue report. The differences you see may be attributable to the number of permutations being done to estimate the...

Dear Teng, Thanks for sharing the geneset and logFC values you were using; very helpful in diagnostics. I've compared the p-values from `bulk.gsea`, `iterative.bulk.gsea` and `gsea` and have found that...

Hi Akdes, The only use of `as.vector()` is in coercing a `table` of either snps or genes frequencies into a `vector`. I've seen similar errors thrown with `as.data.frame()` before when...

Hi Erin, Thanks for the excellent debugging. retestBoundSnps is a boolean parameter that is passed in the built-in function and by default set to TRUE, along with retestBoundGenes. You can...

Hi, Please check that the biomart object you are using is indeed properly loaded. You can double check this by accessing `hb$genes` in the tutorial. Please check that the gene...

Hi, Thanks for the bug report. This may have to do with biomart or a related dependency being updated. To help me with the debugging, could you please let me...

Hi Jocelyn, Thanks for reaching out. Astute observation. The general goal of the filtering is to remove lowly expressed genes that are not well detected in the single-cell data for...