Michael Schubert

Analysis ideas

2

- [x] relationship between signalling footprints and pathway expression - [x] overlap - [x] which signal activates transcription of which pathway? - [x] ~~which pathways are more posttranslationally controlled, which...

quite hard to find a specific script right now

empirical p-values for glmnet multivariate results

1

prerequesites - [x] map all scores to specific set of pathways - [x] use same pathway set input for glmnet kinds of models - [x] pathways - [x] mutations and...

need to impute them using sig-only neighbourhood does that change the assocs? also, speed in general should work better with mutation-heavy tumors and CNA-heavy - can we find something interesting...

app-shells/radian: add ebuild

2

A modern R console

Thanks for creating/maintaining repology including the web app! It's a great tool for me to track the package versions I maintain for the Archlinux AUR to see when I should...

Starting from your "Quick Overview" example (with `plyranges=1.18.0`), ```r library(plyranges) df % select(this_col_does_not_exist) ``` I get the error message: > Error in select_rng(.data, .drop_ranges, ...) : > Cannot select/rename the...

Local processing reports errors only after all calls complete

1

Consider the following function ```r fx = function(x) { if (x %% 2 == 0) warning(paste("warning on", x)) if (x %% 3 == 0) stop(paste("error on", x)) x } clustermq::Q(fx,...

It would be nice if `ggmsa` was able to use alignments from the [`msa`](https://bioconductor.org/packages/release/bioc/html/msa.html) package directly. These are e.g. of class `MsaDNAMultipleAlignment`, which `ggmsa` can not handle. It can, however,...

### Description of the bug I'm trying to process bulk [Smart3-seq data](https://teichlab.github.io/scg_lib_structs/methods_html/SMART-seq_family.html#SMART-seq3) using the pipeline (related Slack discussion [here](https://app.slack.com/client/TE6CZUZPH/CHN5BV5DW)). In my case, the FASTQ read structure is the following: ```...