Deep mutational scanning of SARS-CoV-2 Omicron BA.1 spike using a barcoded lentiviral platform
==============================================================================================

This page documents the data analysis.
For the actual code, see https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS

Study by Bernadeta Dadonaite and Jesse Bloom.

Workflow
--------
Below is the rulegraph for the `snakemake <https://snakemake.readthedocs.io/>`_ workflow.
Click :download:`here <../../results/docs_source/filegraph.svg>` for the more detailed filegraph.

.. image:: ../../results/docs_source/rulegraph.svg
   :width: 800

Analysis notebooks
------------------
Many of the plots in these notebooks are interactive, so try mousing over points for
details, using dropdowns, etc.

.. toctree::
   :maxdepth: 1

   analyze_pacbio_ccs
   build_pacbio_consensus
   build_codon_variants
   analyze_variant_counts
   analyze_func_scores
   fit_globalepistasis
   avg_muteffects
   analyze_prob_escape
   fit_polyclonal
   avg_antibody_escape
   validation_IC50s
   compare_muteffects

Data files
----------
- `parental gene sequence <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/gene_sequence/codon.fasta>`_
- `parental protein sequence <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/gene_sequence/protein.fasta>`_
- `sequential-to-reference site numbers <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/site_numbering/site_numbering_map.csv>`_
- `codon-variant table <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/variants/codon_variants.csv>`_
- `processed barcode sequencing runs <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/barcode_runs/processed_barcode_runs.csv>`_
- `variant counts <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/variant_counts>`_
- `functional selection experiments <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/func_scores/functional_selections.csv>`_
- `mutation effects for each functional selection <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/globalepistasis_fits>`_
- `mutation functional effects replicate average (observed phenotype) <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/muteffects_functional/muteffects_observed.csv>`_
- `mutation functional effects replicate average (latent phenotype) <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/muteffects_functional/muteffects_latent.csv>`_
- `antibody selection experiments <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/prob_escape/antibody_selections.csv>`_
- `antibody escape values <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/antibody_escape>`_
- `sequential to reference site numbering <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/site_numbering/site_numbering_map.csv>`_
- `natural evolution enrichment vs DMS <https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS/blob/main/./results/compare_muteffects/natural_enrichment_vs_dms.csv>`_

Interactive plots of mutation functional effects
------------------------------------------------
- `Observed phenotype effects <muteffects_observed_heatmap.html>`_
- `Latent phenotype effects <muteffects_latent_heatmap.html>`_

Interactive plots of mutation antibody escape
---------------------------------------------
- `268C.59A escape plot <268C.59A_escape_plot.html>`_
- `CC25.103 escape plot <CC25.103_escape_plot.html>`_
- `CC25.43 escape plot <CC25.43_escape_plot.html>`_
- `CC67.105 escape plot <CC67.105_escape_plot.html>`_
- `CC9.104 escape plot <CC9.104_escape_plot.html>`_
- `CC95.102 escape plot <CC95.102_escape_plot.html>`_
- `LyCoV-1404 escape plot <LyCoV-1404_escape_plot.html>`_
- `NTD 5-7 escape plot <NTD_5-7_escape_plot.html>`_
- `SD1 12-19 escape plot <SD1_12-19_escape_plot.html>`_

Additional plots
----------------
 - `natural enrichment versus DMS <natural_enrichment_vs_dms.html>`_