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10x Genomics
Chromium Single Cell Gene Expression

What is Cell Ranger?

Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. There are two pipelines:

These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, and HTML formats that are augmented with cellular information.