Gregor Sturm

In GitLab by @szabogtamas on Jan 24, 2020, 20:14 As to the lacking chains: I would just mark them with 'XXXXXXXXXXXXXXXX' just like for sequence alignment. But this is only...

Possibly also include V & D genes into sequence logo. Example from Dash et al. (2017): 

Hi @willblev, thanks for reporting this issue! While I think I can easily find a workaround for the Biopython issue, the second part looks a little more sinister. Essentially, the...

I started looking into this and it seems it is becoming increasingly difficult to keep the read_tracer function working. * As you already figured out, the `pkl` files won't load...

> Which was the last supported version of TraCeR? The version I have been successfully using was built using this Dockerfile based on the `teichlab/tracer:latest` two years ago: https://github.com/icbi-lab/smartseq2_pipeline/tree/master/Docker/tracer However...

In GitLab by @grst on Mar 26, 2020, 18:40 One way to visualize this is to plot a clonotype network and color it by sample. Another could be `upsetplots` as...

Pinging @ktpolanski, who added the Hamming Distance Feature: What do you think about the normalization? --- Regarding the `DistanceCalculator`: What's your question in particular? I think it should be feasible...

Suggestion: Implement a "getter" class that supports method chaining. putative API: ```python # get a series (n_obs, ) ir.get(adata).airr("locus", "VJ_1") # get most frequent C gene ir.get(adata).airr("c_call", "VJ_1").most_frequent(n=10) # get...

Issues: * the `top_n` doesn't generalize well. What if you want an airr variable sorted by clonotype modularity? Or a column from another mudata modality? In most cases you'd be...

For the convenience functions ```python ir.get.most_frequent(adata.obs["clonotype"]) ``` is more flexible, as it can be applied to any pandas series. Also one that was retrieved from the airr data, e.g ```python...