Zewen Kelvin Tuong

icon indicating an email [email protected]

icon company The University of Queensland icon location I'm a Group leader at The University of Queensland on Pediatric Systems Immunology and I use R and python to analyse lots of single-cell RNAseq data

Results 56 comments of Zewen Kelvin Tuong

scverse datastructure for AIRR data

all of this sounds awesome. Just have some naive question about how well/fast does it deal with situation when there's >100k+ cells? would `chains_as_awkarr` take a while to retrieve the...

Normalized Hamming Distance

> Does normalisation imply dividing by the length of the sequence? If so, then that puts us pretty close to what Dandelion does, no? This would put it more in...

[feature request] Update existing docstring

would love to see this too!

IEDB database cdr3_aa stored as junction_aa

> junction_aa -> cdr3 should be trivial, right? Just clip off the first and last amino acid. Any caveats? yes should be correct. > cdr3 -> junction_aa: Is it correct...

IEDB database cdr3_aa stored as junction_aa

Looks like they are correct and are treated as exceptions, but probably non-functional For TRAJ35*01: ``` (6) noncanonical J-MOTIF: Cys-Gly-X-Gly instead of Phe-Gly-X-Gly. The functionality of TRAJ35*01, initially considered as...

IEDB database cdr3_aa stored as junction_aa

i just checked the IgBLAST auxiliary files that indicate where the CDR3 end is and crossed it to the fasta files and it looks like the codons are correct for...

Restore global pairwise distance calculation

this might be a partial solution to #219, can use umap afterwards?

scrublet doesn't work properly

I also experienced this and managed to solve this by downgrading `annoy` to `1.16.3`.

'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte

Hi @rachel662, what is your h5py version?

problems with plot_cpdb using cellphonedb v5 outputs

Hi, you are using the wrong input for this. your `means` looks like it's `deconvoluted`.