V2 beta #278
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V2 beta #278
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Make package more in line with standard R package practisces
… param to scatterClonotype, added more vdiffr tests
Added vdiffr into testing, nessecary files for Rcpp, seurat command, and minor syntax changes
Adding Qiles work to v2
Redid the contig list and seurat sample to reduce overall size and have the most up-to-date seurat version object. Changed the corresponding references in .R files and separated out functions in .R files with multiple exported functions
Remove extra barcode addition to meta data
modify signposts to actual function calls
Remove vegan call and wrote custom functions, expand metrics
Using switch function now for different indices and added cosine similarity
No use any color built into grdevices hcl.pal() function
…it in helper-testing_functions.R, added v2 to Rcmd check workflow
Sped up testing and AA kmer counting (with Rcpp)
Still have issues with clonalNetwork
massively sped up `combineTCR` with Rcpp
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