software

I created and maintain these software repositories

dsb

dsb: a method for normalizing and denoising antibody derived tag data from CITE-seq, ASAP-seq, TEA-seq and related assays.

The dsb R package is available on CRAN: latest dsb release
to install in R: install.packages('dsb')

This method is described in Mulè, Martins, and Tsang, Nature Communications (2022)

Vignettes:

1. Using dsb in an end to end CITE-seq workflow including WNN clustering
   
2. How the dsb method works
   
3. Normalizing ADTs if empty drops are not available
   
4. FAQ etc.

dsb is also available in Python through muon

scglmmr

scglmmr: sample-level single cell generalized linear mixed models and phenotype networks in R

scglmmr is an R package for implementing mixed effects models on single cell data with complex experiment designs.

The scglmmr R package is available on Github: latest scglmmr release
to install in R devtools::install_github(repo = "https://github.com/MattPM/scglmmr")