Mikhail Shugay

Ambiguity between query/target in docs

1

Read sequence is called ``targetSequences`` in the output. While in the mutation format description in docs we have " Mutations are encoded as a list of single-nucleotide edits (similar to...

Add an explicit flag specifying that a CDR3 region is canonical

1

Needed for coding CDR3s only. Basically we need to check the following two things: * First and last codons are the reference ones (i.e. CDR3 is not trimmed in any...

E.g. a prior to exclude certain D-J combinations

- 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

Sample pool

1

Implement sample pool (mass join) Total diversity estimate for a population of samples using Chao2

- Add R wrappers for most useful VDJtools output types - Refactor existing scripts based on them - Add R template demonstrating running VDJtools and managing metadata

Add R scripts for - Clonal homeostasis - PCA based on V/J usage profiles - A plot for sample pool #3 - Visualize overlap between up to 10 repertoires in...