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Add a warning that -*-protocol options and seq_type differ (at least for tumour). To ensure seqtype WXS doesn't get WGS as SAMPLE protocol set in the VCF.
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@edmundmiller and friends :)
this is a placeholder to collect ideas to realise additional tutorials on use-cases of sarek
Variant Calling is currently being integrated (http://lescai-teaching.github.i…
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Also need to decide how to handle multi (>2) sample VCFs, e.g. if you have 10 tumour samples in 1 VCF (not sure how common this is out in the wild)
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[Create synthetic dataset for this paper Integrating spatial gene expression and breast tumour morphology via deep learning](https://www.nature.com/articles/s41551-020-0578-x)
Found from Aquila:
h…
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Sorry
Long time I am struggling how to provide GISTIC required input like `Num_Probes` and `Segment_Mean`
I have called somatic copy number by `scatngs` and I have copy number output file (attach…
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Since the Node/Edge Services are completed we need to test the viability of the pipeline connections. We wil hardcoded a pipeline and have it use all the services to verify that each piece is workin…
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https://www.nature.com/articles/s41586-019-1382-1
The study is already in private portal, but may require some curation. Please check with Taylor lab before pushing out.
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jjgao updated
2 years ago
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From first tumour: will be choosing 10s saturation pulse.
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Normal tissue complication probability (NTCP), tumour control probability (TCP)
Migrated from https://app.assembla.com/spaces/slicerrt/tickets/122-compute-ntcp-and-tcp-metrics/details
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Croucher et al.
Single-cell transcriptional analysis of the immune tumour microenvironment during myeloma disease evolution
https://www.biorxiv.org/content/10.1101/2021.10.22.464971v1.abstract
Da…