Here we will list tools and packages from friends and collaborators that are useful for CITE-seq. If you want to share a piece of code with us don’t hesitate to contact us.

Rahul Satija’s lab (NYGC & NYU) has developed tools for read level processing of CITE-seq data (listed below) and has recently update their Seurat package to support multimodal data. You can download Seurat, and follow tutorials through Rahul’s website.

Read-level processing and other tools

  • CITE-seq-Count developed by Christoph Hafemeister and Patrick Roelli, can be used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build a count matrix.



  • For Cell Hashing, we recommend using the Cost per cell calculator from the Satija Lab to plan experiments, determine number of hashes, number of cells to load, expected doublet rates (detected and undetected) and cost considerations.