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data sensitivity analyses and dependencies added Jun 21, 2019
passage_predictions
phylogenetic_analysis description of Figures 3-7, SuppFig2 with necessary code Jun 11, 2019
sensitivity_analyses
shiny_app descriptions polished Jun 21, 2019
surveillance_analysis description of Figures 3-7, SuppFig2 with necessary code Jun 11, 2019
virus_production_rates
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ANP_model.R
README.md

README.md

Profiling the Host ANP32A Splicing Landscape to Predict Influenza A Virus Polymerase Adaptation

Authors: Patricia Domingues, Davide Eletto, Carsten Magnus, Hannah L. Turkington, Stefan Schmutz, Osvaldo Zagordi, Matthias Lenk, Michael Huber, Martin Beer, Silke Stertz, Benjamin G. Hale


Description

This repository contains code and data to repeat and extend the analyses of "Profiling the Host ANP32A Splicing Landscape to Predict Influenza A Virus Polymerase Adaptation" by Domingues, Eletto, Magnus et al (2019). In addition, it contains all necessary code to generate the shiny app on your machine. The analysis was implemented in the freely available R programming language.


Analyses

We stored the code into different folders according to the respective analyses:

  1. Phylogenetic analysis of ANP splice regions (/phylogenetic_analysis/)
  2. Estimation of virus production rates and bootstrapping. (/virus_production_rates/)
  3. Passage prediction and risk scores (/passage_predictions/)
  4. Heatmaps and shiny app (/shiny_app/)
  5. Statistical analysis of surveillance data (/surveillance_analysis/)
  6. Sensitvity analyses (/sensitivity_analyses/)

Folder 1 contains the .xml file to repeat the phylogenetic analysis, this file also contains the sequence alignment. Folder 4 contains more detailed instructions on how to set up the shiny app for interactive heatmaps and on how to generate customized heatmaps. Additional data is stored in the data folder which consists of one folder with input data and one folder of results of the modelling procedures that are time intensive to produce.


Figure plotting

Besides being able to use our modeling framework for analyses of newly collected data on ANP32A splice variants or Influenza sequences found in mammalian/avian species, this repository also contains information on how to reproduce the figures of the paper "Profiling the Host ANP32A Splicing Landscape to Predict Influenza A Virus Polymerase Adaptation". Graphs in Figures 1, 2 and Supplement Figure 1 are produced in Prism based on the data accompying the original paper. The remaining figures include more complicated modeling and can be obtained in the following way:

Figure How to
3e Phylogenetic analysis with BEAST2 with the .xml file Flu_ANP32A.xml. The maximum clade credibility tree can be obtained by TreeAnnotatar and FigTree.
4b-d, f, g function calls explained in display_bestestimates_CI.R
5, SuppFig 2 function calls explained in passage_predictions_risk_scores.R
6a function calls explained in passage_predictions_risk_scores.R
6b function calls explained in heatmap.R
7 function calls explained in host_adaptation.R
SuppFig 3 function calls explained in sensitivityanalyses.R

Issues

If you encounter any bugs or have any specific questions about the analysis, please file an issue.

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