Cell Ranger ARC

type access

  • Operating System:

  • Terminal:

  • Shell:

  • Editor:

  • Package Manager:

  • Programming Language:

  • Utility:

Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression (GEX), chromatin accessibility, and their linkage. Furthermore, since the ATAC and GEX measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and GEX.

For more information, check here.

Cell Ranger ARC Utilities
  • aggr

  • count

  • mkfastq

  • mkgtf

  • mkref

  • reanalyze

  • terminal

Terminal session

The Cell Ranger ARC: terminal utility allows the user run the different Cell Ranger ARC pipelines via command line by clicking on the button

User interface

When available, the --uiport=3600 option enables the pipeline's visual user interface (UI), accessible through the button


The UI port must be 3600.