Deep mutational scanning of HIV Envelope BF520 with anti-CD4 binding site sera and antibodies
=============================================================================================

This page documents the data analysis.
For the actual code, see https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera

Study by Caelan Radford, Jesse Bloom, et al. See the pre-print here (https://www.biorxiv.org/content/10.1101/2023.03.23.533993v1).

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_func_scores
   fit_globalepistasis
   avg_muteffects
   analyze_variant_counts
   analyze_prob_escape
   fit_polyclonal
   avg_antibody_escape
   validation_ICs
   mutations_vs_natural_sequences

Data files
----------
- `parental gene sequence <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/gene_sequence/codon.fasta>`_
- `parental protein sequence <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/gene_sequence/protein.fasta>`_
- `sequential-to-reference site numbers <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/site_numbering/site_numbering_map.csv>`_
- `codon-variant table <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/variants/codon_variants.csv>`_
- `processed barcode sequencing runs <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/barcode_runs/processed_barcode_runs.csv>`_
- `variant counts <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/variant_counts>`_
- `functional selection experiments <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/func_scores/functional_selections.csv>`_
- `mutation effects for each functional selection <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/globalepistasis_fits>`_
- `mutation functional effects replicate average (observed phenotype) <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/muteffects_functional/muteffects_observed.csv>`_
- `mutation functional effects replicate average (latent phenotype) <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/muteffects_functional/muteffects_latent.csv>`_
- `antibody selection experiments <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/prob_escape/antibody_selections.csv>`_
- `antibody escape values <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/antibody_escape>`_
- `sequential to reference site numbering <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/site_numbering/site_numbering_map.csv>`_
- `PDB with 1-18 escape values as b factors <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/escape_PDBs/1-18_epitope_1.pdb>`_
- `PDB with 3BNC117 escape values as b factors <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/escape_PDBs/3BNC117_epitope_1.pdb>`_
- `PDB with PGT151 escape values as b factors <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/escape_PDBs/PGT151_epitope_1.pdb>`_
- `PDB with IDC561 escape values as b factors <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/escape_PDBs/IDC561_epitope_1.pdb>`_
- `PDB with IDC513 escape values as b factors <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/escape_PDBs/IDC513_epitope_1.pdb>`_
- `PDB with IDC508 escape values as b factors <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/escape_PDBs/IDC508_epitope_1.pdb>`_
- `PDB with IDF033 escape values as b factors <https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera/blob/main/./results/escape_PDBs/IDF033_epitope_1.pdb>`_

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
---------------------------------------------
- `1-18 escape plot <1-18_escape_plot.html>`_
- `3BNC117 escape plot <3BNC117_escape_plot.html>`_
- `IDC508 escape plot <IDC508_escape_plot.html>`_
- `IDC513 escape plot <IDC513_escape_plot.html>`_
- `IDC561 escape plot <IDC561_escape_plot.html>`_
- `IDF033 escape plot <IDF033_escape_plot.html>`_
- `PGT151 escape plot <PGT151_escape_plot.html>`_