Run Cell Ranger tools using cellranger_workflow
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**cellranger_workflow** wraps Cell Ranger to process single-cell/nucleus RNA-seq, single-cell ATAC-seq and single-cell immune profiling data, and supports feature barcoding (cell/nucleus hashing, CITE-seq, Perturb-seq). It also provide routines to build cellranger references.

A general step-by-step instruction
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: general_steps.rst

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Single-cell and single-nucleus RNA-seq
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: sc_sn_rnaseq.rst

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Feature barcoding assays (cell & nucleus hashing, CITE-seq and Perturb-seq)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: feature_barcoding.rst

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Single-cell immune profiling
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: sc_vdj.rst

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Single-cell ATAC-seq
^^^^^^^^^^^^^^^^^^^^

.. include:: sc_atac.rst

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Single-cell Multiome (GEX + ATAC)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: sc_multiome.rst

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Flex, Sample Multiplexing and Multiomics
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: multi.rst

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Build Cell Ranger References
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. include:: build_refs.rst