vdjtools
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mikessh
Post-analysis of immune repertoire sequencing data
Hi. I would like to use this function with a dataset That is not a vdj one. I have longer aa sequences and read prop, read count and sample info....
As like the Tabular output of CalcBasicStats, I think it's quite necessary to know how do you calculate some parameters, as mean_frequency, convergence et al. to help us to interpret...
Hi, when you have a chance, could you please add module for clone clustering like migmap does? It will be great if output data from vdjtools can be imported to...
Hey, I came across this negative value for the "NonOverlapping" part in the paired.strict.table.collapsed.txt which in turn leads to a large white area in the abundance plot for that sample...
No information is provided on the VDJ tools documentation regarding the details of the analysis output for the clonotype tracking heatmap function. The output graph key simply says "value" not...
Would one of the developers please develop a parser for TRUST? Thanks. https://bitbucket.org/liulab/trust/ https://www.nature.com/ng/journal/v49/n4/pdf/ng.3820.pdf
Hi Mikhail and @antigenomics team! Have really enjoyed using VDJTools so far for human data. Had to do a vanilla install of R 3.3.0 to get it working on my...
- Both amino acid and nucleotide - Only basic implementation, e.g. XGGXX; more complex searches should be done via `cdr3align` - (?) Additional filters, e.g. V/J/CDR3 length
**Clonotypes and frequencies**: - Re-normalizing sample - Collapsing duplicates **Segments**: - Re-calculating V/D/J boundaries (requires a built-in aligner) - Refinement/de novo of D mappings
Implement sample pool (mass join) Total diversity estimate for a population of samples using Chao2