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# Parsimony Diversity Exploration
We've been exploring the parsimony diversity of our simulated data, and trying to understand how various parameters of the simulation affect this summary statistic…
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The data frames stored under `GAMBLR.data::somatic_hypermutation_locations_GRCh37_v*` have chr prefixing in the chromosome column, which creates a lot of extra work to handle in most instances. Also t…
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Possibly using something like BASELINe or this: http://arep.med.harvard.edu/pdf/Uduman_jimm_13.pdf
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Hi Quentin,
According to your published article, How could you find out and extract the non-productive sequences (for new model construction) from the raw data? Do you have any good ideas?
In …
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https://www.nature.com/articles/s41586-020-2209-9
- [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this ch…
jjgao updated
2 years ago
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Hi,
I am having some trouble using hyperfreq with some samples in which a large percentage of the sequences are hypermutated. I assume it is because of the consensus sequences that they are compared …
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## 🚀 Feature
Most BCR analysis programs (ex. MIXCR and IMMCANTATION) also output a field with information regarding the constant chain (ex. IGHG1, IGHA1). It would be nice to also load that info…
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Hi Bram,
I am using RTCR to identify the TCR repertoire from amplicon sequencing. I have some more question abouts the output result.
1) how can get the mapping rate for the fastq reads (MiSeq, …
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How to do somatic hypermutation analysis between two sample sets (3 samples per cohort) Can we do somatic hypermutation analysis from https SMARTer Mouse TCR a/b Profiling Kit? I came across "B cell l…
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Hi,
command,
mixcr exportClones -vIdentityPercents -vBestIdentityPercent -dIdentityPercents -dBestIdentityPercent -jIdentityPercents -jBestIdentityPercent test.contigs.clns clones.tsv
clones_IG…