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I get this error when running the parser with facets.tsv file. In my tsv file i have these columns:
Traceback (most recent call last):
File "/Users/adhisadi/workspace/analysis/parse_cnvs_fac…
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Hi
I am trying to build the models for my MSI sites.
Wondering how to train models for specific panel as you provided in your repo, since the tool did not provide any command to generate ones, and…
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Hi!
Is there a way to do somatic calling on multiple samples at once? I have multiple samples from different areas in a tumor of a patient. As part of a phylogenetic analysis, I would like to call th…
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Hello, I'm working with data from multiple patients and I'm wondering if infercnv has a way to handle paired tumor/normal from across multiple patients + healthy donors. Some patients contribute both …
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Dear Antonio, I'm using your fantastic tool for the analysis of a melanoma single cell datasets. Everything works just fine, except for a sample. Its the same cell line with different treatments, almo…
pgm99 updated
7 months ago
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When I ran Msisensor, I found the results are quite different between using the deduplicated bam and not deduplicated bam. I wonder which bam shoud be used , the deduplicated bam or not deduplicated …
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https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1002309
Data seems to be available at : https://github.com/hammerlab/multi-omic-urothelial-anti-pdl1 & https://zenodo.org/reco…
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@davidbenjamin We might be able to share some code with contamination calculation, etc. Tangentially related, we also should unify the pileup-based tools at some point. Low priority, we can discuss …
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I am wondering if it's possible to get the data of the UK NLMT study? There are some overlaps with the TRACERx datasets. It would be very interesting if we can get the response data.
https://www.na…
jjgao updated
2 years ago
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https://www.nature.com/articles/s41588-020-0628-z
This is a meta analysis paper. The authors assembled data from other papers and reprocessed them. It would be good idea to identify the source stud…
jjgao updated
2 years ago