Deep mutational scanning (DMS) pipeline for a viral entry protein (VEP)
=======================================================================

This page documents the data analysis.
For the actual code, see https://github.com/dms-vep/dms-vep-pipeline

Study by Jesse Bloom.

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_func_scores
   fit_globalepistasis
   avg_muteffects
   analyze_variant_counts
   analyze_prob_escape
   fit_polyclonal
   avg_antibody_escape

Data files
----------
- `parental gene sequence <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/gene_sequence/codon.fasta>`_
- `parental protein sequence <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/gene_sequence/protein.fasta>`_
- `sequential-to-reference site numbers <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/data/site_numbering_map.csv>`_
- `codon-variant table <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/variants/codon_variants.csv>`_
- `processed barcode sequencing runs <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/barcode_runs/processed_barcode_runs.csv>`_
- `variant counts <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/variant_counts>`_
- `functional selection experiments <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/func_scores/functional_selections.csv>`_
- `mutation effects for each functional selection <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/globalepistasis_fits>`_
- `mutation functional effects replicate average (observed phenotype) <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/muteffects_functional/muteffects_observed.csv>`_
- `mutation functional effects replicate average (latent phenotype) <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/muteffects_functional/muteffects_latent.csv>`_
- `antibody selection experiments <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/prob_escape/antibody_selections.csv>`_
- `antibody escape values <https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/antibody_escape>`_

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
---------------------------------------------
- `REGN10933 escape plot <REGN10933_escape_plot.html>`_
- `REGN10933 icXX plot <REGN10933_icXX_plot.html>`_
- `S2M11 escape plot <S2M11_escape_plot.html>`_
- `S2M11 icXX plot <S2M11_icXX_plot.html>`_