Mikhail Shugay
Mikhail Shugay
Actually the full list of what is needed (i.e. observed in lymphoma samples): * Vd-Dd3, Dd2-Jd * Dd-Ja * Dh-Jh * More complex: Dd2-Dd3, Vk-KDE, INTRON-KDE (IGK) here ``d,a,h,k`` stands...
To speed up it is reasonable to suggest that best D match cannot be more than 30 bases from the available reference point
Quite complex but yes.. also the frame (0-2) at conserved Cys. The "Pseudo V/J" is what I asked for. Three flag states `1`, `0` and `NA` are OK. If at...
Hi, have you checked if there is ``"IGHJ4 "`` in your data? I.e. IGHJ4 with space after the segment name
The Z scores are computed by the ``heatmap.2`` function that makes the plot (see e.g. https://www.rdocumentation.org/packages/gplots/versions/3.0.1/topics/heatmap.2). Typically for a vector X one can obtain Z scores by normalizing them to...
Sample pool implemented, some plotting stuff (e.g. power law/chao2) is needed
Hi, can you confirm that your clonotype table have frequencies that 1) sum to 1, 2) are strictly positive?
Hello! I don't think this is mouse-specific as VDJtools is neutral to species and receptor chain. Can you please post a few good and bad examples here? It is better...
Hello! Unfortunately this option was removed quite a while ago, so its a bit tricky. You can do this by modifying the R script (file with ``*.R`` extension) produced by...