Hi Bioinformatics lovers,
I put together 4 blog posts on CITE-seq analysis:
Part 1 How to use Salmon/Alevin to preprocess CITE-seq data https://divingintogeneticsandgenomics.com/post/how-to-use-salmon-alevin-to-preprocess-cite-seq-data/
Part 2 CITE-seq downstream analysis: From Alevin output to Seurat visualization https://divingintogeneticsandgenomics.com/post/cite-seq-downstream-analysis-from-alevin-output-to-seurat-visualization/
Part 3 Centered log ratio (CLR) normalization for CITE-seq protein count data https://divingintogeneticsandgenomics.com/post/details-in-centered-log-ratio-clr-normalization-for-cite-seq-protein-count-data/
Part 4 CITE-seq normalization using empty droplets with the dsb package https://divingintogeneticsandgenomics.com/post/part-4-cite-seq-normalization-using-empty-droplets-with-the-dsb-package/
Happy Learning! Tommy
