Currently, immune-deconvolution uses only the xCell method. This method reports relative scores without units and only allows for comparisons between samples, but not between cell types (see #1234).
We may want to have a complementary method, such as quanTIseq, which provides absolute scores that can be interpreted as fractions of the sample containing that cell type. Further, these scores can be compared both across samples and cell types.
What changes need to be made? Please provide enough detail for another participant to make the update.
Integrate quanTIseq into the immune-deconvolution in addition to xCell, using the same immunedeconv package.
What input data should be used? Which data were used in the version being updated?
v21
When do you expect the revised analysis will be completed?
jharenza
commented
2 years ago
What analysis module should be updated and why?
Currently,
immune-deconvolutionuses only thexCellmethod. This method reports relative scores without units and only allows for comparisons between samples, but not between cell types (see #1234).We may want to have a complementary method, such as
quanTIseq, which provides absolute scores that can be interpreted as fractions of the sample containing that cell type. Further, these scores can be compared both across samples and cell types.What changes need to be made? Please provide enough detail for another participant to make the update.
Integrate
quanTIseqinto theimmune-deconvolutionin addition toxCell, using the sameimmunedeconvpackage.What input data should be used? Which data were used in the version being updated?
v21When do you expect the revised analysis will be completed?
1-2 days
Who will complete the updated analysis?
@sjspielman