Dr. Jens Preußner

Hi all, we recently noticed that Capsule fails to parse the java version string from `java -version` in the OpenJDK build from [Azul Zulu](https://www.azul.com/downloads/zulu/). The problem is that the version...

Suspected error in pagoda.show.pathways

2

See https://groups.google.com/d/msg/singlecellstats/tqvc3cr-8Hs/7P3PRfdZCQAJ for further explanation. Best, Jens

Allow pagoda.reduce.loading.redundancy to be used with custom colors

2

Hi Jean and Peter, I would like to see the clustered aspects of pagoda.reduce.loading.redundancy() in custom colors (from RColorBrewer). Unfortunately, pagoda.reduce.loading.redundancy doesn't know in advance how many clusters will be...

How to deal with batch effects?

2

Thank you for the great contribution! I'm currently trying scHPF on a few datasets and found that it was easy to apply. I'd like to know how to properly deal...

Hi Gabriel, thanks for `switchr` - it has been proven very useful in my day-to-day work. Currently, I have a seeding manifest defined in my global `.Rprofile` on which every...

Demultiplexing from barcodes in headers

9

Hi Joe, I just run across a `Segmentation fault.` error, when demultiplexing from barcodes in the header. However, all `%.fastq.gz` files are created as empty files, so the error must...

Typo in Cj specs (4.2 data)

2

Hi Mike, I noticed a little typo in the Cj specs[1]. In section 4.2 data, it says: Each object **is** MAY have any of three possible properties Should be: Each...

Logical status leads to strange plot

1

Hi Michael, when using a logical status in geom_kmticks like ``` r library(ggkm) data(lung) lung$status2 = ifelse(lung$status == 1, TRUE, FALSE) ggplot(lung, aes(time = time, status = status2)) + geom_km()...

Better 10X support (was Possibility to do QC only on one pair?)

7

Hi HTStream-Team, is it possible to use your toolkit in paired-end mode, but actually apply QC functions (polyATrim, QWindowTrim) only on one pair (e.g. R2)? I'm asking because I tried...