Dave Tang

Check the class of the universe vector (and your gene vector) and make sure the class is `character`. For example: ```r enricher( gene = as.character(dge$entrezgene_id), TERM2GENE = pathway.p, universe =...

Hi, I'm just trying to follow the tutorial (http://hms-dbmi.github.io/scde/diffexp.html) but when I get to the "Fitting error models" step [using the scde.error.models() function], I get an error (despite using `flexmix_2.3-13`):...

Hi Jean, thanks for the reply. I tried the example code for `knn.error.models` but I still got a similar error: ``` library(scde) data(pollen) cd

Hi Jean, I just used the newest [Docker Container](https://hub.docker.com/r/bioconductor/release_core2/) and repeated the steps above. I get a different error with `knn.error.models`: ``` download.file(url = "https://github.com/hms-dbmi/scde/archive/1.99.2.tar.gz", destfile = "1.99.2.tar.gz") install.packages("1.99.2.tar.gz", repos...

I came across this problem when using `bcftools merge` on some Mutect2 VCFs and [as suggested](https://github.com/broadinstitute/gatk/issues/6857#issue-712317320), a quick fix is to change `AS_FilterStatus` in the VCF header. However I changed...

The article was interested in calculating $\frac{\delta L}{\delta w_1}$, which tells us how loss changes with respect to $w_1$. Using the chain rule, this becomes: $$ \frac{\delta L}{\delta w_1} =...

Split your genome up into chromosomes (or contigs), run `dwgsim` on each separately, and then concatenate the FASTQ (and mutation) files. If you didn't already know, you can directly `cat`...

I'm interested in contributing but will need some guidance. The Docker Hub link above for Aspera no longer exists, so I wrote my own [Dockerfile](https://github.com/davetang/learning_docker/blob/main/aspera_connect/Dockerfile) and pushed it to [Docker...

I have never built a Conda package before but I've always wanted to find out how. I just found https://anaconda.org/hcc/aspera-cli and will check it out first.

Hi @dtm2117, I got several messages recently about issues with RStudio Server and I just wrote a [blog post](https://davetang.org/muse/2023/02/24/running-rstudio-server-with-r-4-2-2-with-docker/) about it. I think you can now exclude the following parameters...