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What is

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Cell Ranger?

Enrichment analysis is a technique commonly used to add biological context to a list of genes, such as list of significant genes. The procedure is based on assigning genes to groups and then finding overrepresented groups in filtered gene lists using a Fisher's exact test.

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Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis  for 10X Genomics Chromium Technology[1].

Cell ranger in Flow

Cell Ranger v6.0.0[2] has been wrapped In Partek Flow. It does not comprehensively cover all of the options and analysis cases Cell Ranger can handle, but converts FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, UMI counting. The output gene expression count matrix in .h5 format (both raw and filtered) then becomes the starting point for downstream analysis for scRNA-seq in Flow.

Running Cell ranger in Flow

We recommend filtering to a set of genes you want to test for enrichment, but Gene set enrichment will run on any Feature list data node. 

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