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hello,
I just ran some RNASeq data with ImRep. Compared with TRUST and mixcr. Thanks to your wonderful work, this program runs really fast!
But when I tried to the the compare.repertories.py, I …
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This issue have been created to discuses the possible future expansion of the openMINDS-chemical extension. For the moment following schema are under study :
### tracingAgent
property | count | va…
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This is something I've been doing off-bcbio for quite a while and I think it would be worthwhile to streamline. I would like to use this issue to collect information on how people have been doing thei…
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### Summary
Our new normalization procedure should recapitulate expected treatment differences with respect to clonality, abundance, and other diversity measure of TCR repertoires. In addition, biolo…
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Hello
By `393472 SNPs` for `17 samples`, after running your software I am getting `600 clonal variants and 83 sub-clonal` the rest are NA
Do you think something is going wrong with my data?
H…
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Hi
I need your personal point of view please
I have two `bulk RNA-seq` patients (PBMC) on which I run `mixcr`
For the same two patients I have `5' single cell` on which I run `TRUST4`
I a…
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Hello
I am trying to figure out how I can get the `ntot` required for clonality analysis
I have `ploidy`, `purity`, `major` and `minor allele copy number`
I googled for `ntot` which googling …
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Currently, for MSK IMPACT, we have mutations, CNAs and fusions/SVs, but we have many additional types of derived data generated by CMO.
- Mutational signatures
- HLA types
- HLA LOH
- Genomics-i…
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Ahead of supporting [Sequenza](http://www.cbs.dtu.dk/biotools/sequenza/) clonality estimation (#200) and segmentation (#198), let's just try exporting a .cnr and VCF file to Sequenza's input format, w…
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Hi, thanks for providing the software.
I have multiple samples and have run TRUST on each of them, but the sequencing depths are different between samples, do you think there is a suitable solution …