Christian Rohde

color code for HeatmapAnnotation/top_annotation changes and is inconsistent. Is the a option to mimic pheatmap here?

4

Hi, is it possible to control the HeatmapAnnotation colors for the top_annotation in a similar way that I get colors with pheatmap? I created a shiny were one can select...

Hi, I used TCGAbiolinks to download mutations from the TCGA-LAML cohort. This is my code: `query

Empty 't_depth' 't_ref_count' 't_alt_count' from VCF with format GT:GL:GOF:GQ:NR:NV

1

Hi, I have a kind of similar issue as in https://github.com/mskcc/vcf2maf/issues/332. I noticed this problem earlier and fixed the non matching names with previous data. Now I have the problem...

HGVSc + HGVSp + HGVSp_Short not available after vcf2maf from an annotated VCF from sarek with VEP v108

5

Hi, I am running vcf2maf installed from conda. I skip VEP, since I prepared the VEP annotated VCF with sarek (https://nf-co.re/sarek/3.2.1/usage). Here the VEP version used is 108. The problem...

Hi there, I have a question/suggestion about the MOFA2::calculate_contribution_scores function which "calculates, *for each sample* how much each view contributes to its location in the latent manifold". This was exactly...

model_opts$spikeslab_weights <- TRUE

3

Hi there, it took me a while to understand why my MOFA2 analyses with version 1.4.0 are so different from 1.8.0. With the latest version I had to manually add...

Incompatible OSP file from 2021? Are there changes which could be converted?

3

Hi, I want to edit an old project from 2021 which was saved in .osp format and all data is available in same structure. All videos and photos are loaded...

IntaRNA --version does not reflect the installed conda package version?

3

Hi, I installed IntaRNA with "conda create --name IntaRNA bioconda::intarna". It looks fine if I check the installed packages: ``` conda list -n IntaRNA packages in environment at /home/user/conda/envs/IntaRNA: Name...