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#### What analysis module should be updated and why?
module: fusion_filtering
background:
We had previously implemented filtering in 04-project-specific-filtering.Rmd as a last step to remove…
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Hi Sigve,
Just wondering how you put together a list of tumor suppressors and oncogenes?
A coding variant in EHD2 has downgraded from TIER3 to TIER4 compared to PCGR 0.8.0:
And I susp…
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#### What analysis module should be updated and why?
1) During project specific filtering I mistakenly removed "other" fusions while filtering on column Fusion_Type for putative-oncogene fusion l…
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Hi,
While running the program and under simFeatures creation, I am encountering the following error. please let me know what's the issue and how best it can be resolved.
Thanks a lot for your kin…
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There’s some weird spacing issues - for example here, there’s a ton of whitespace between “activated oncogenes”, “senescence” and “apoptosis” and the respective arrows. and also the arrow for “apopto…
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The idea would be to visualize trends of deletions / amplifications in each of the cancer types (where relevant). Pointing out highly amplified/deleted regions with oncogenes/tumor suppressors may be …
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Hi, daniel
How to turn off the deduplication function of fusioncatcher? I can't find any parameter to set it. In our case, we first use primers to amplify the RNA, then PCR and sequence it, so we d…
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Hi
I have noticed a very informative plot in google
Given a group of samples and a list of genes for which we have mutation and GISTIC data enriched in 2 pathways like cell cycle and p5…
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Hi, I've just installed bioservices through conda (and I've tried pip as well) and I'm following the tutorials. When I tried the **'u.mapping("ACC", "KEGG_ID", query='P43403')'** command, I either get…
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while looking into #1159, I noticed that these three nodes in KG2.3.4 have the name "LAP", but the first item in their `synonym` fields is TGFB_, which seemed slightly odd. then I noticed that if you …