Basic usage

List all available commands

make help

methods

The metafetch python package is stored in src and can be used to interact with the Ireceptor airr commons api. I do plan to make it usable as a module.

Metadata was downloaded from ireceptor gateway using the "human" and "IGH" filters.

ireceptor-number-of-subjects.py counts the number of subjects for each experiment and sorts them from largest to smallest.

immcantation methods

detailed instructions here

Current method for using the immcantation is to use the docker container. I plan on making a functional flake for it as well, but may need to examine the docker image to get full dependency list.

The dockerfile itself isn't very helpful. I think they construct it manually? Very weird.

Links to papers with IGH

• https://pubmed.ncbi.nlm.nih.gov/35943978/ 95

  • 95 subjects
  • Some are patients treated for covid
  • 43 Sero(-)
  • 20 Sero(+)
  • supplemental table has pdf metadata
  • extract metadata
  • genomic DNA

• https://pubmed.ncbi.nlm.nih.gov/23742949/ 76

  • 13 healthy subjects

• https://pubmed.ncbi.nlm.nih.gov/20161664/ 56

• https://pubmed.ncbi.nlm.nih.gov/32668194/ 35

• https://pubmed.ncbi.nlm.nih.gov/28959265/ 25

nextflow pipeline

https://nf-co.re/airrflow/4.2.0