CoV

This dashboard makes it easy to manipulate patient info with sequencing data of the COVID-19 pandemic and display it as chronology, summary tables and phylogenic trees

Input files

1]. annotation : Table with your annotation (the header is required, but the order of the columns can change)

• name : name of the sequence. Any alphanumeric string. Should refer to name used in alignment tree newick file
• virus : name of the virus. Any alphanumeric string. Default="sars_cov_2
• clade : name of the clade. According to nexstrain nomenclature (https://clades.nextstrain.org/)
• pangolin_lineage : name of the clade. According to Pangolin nomenclature (https://pangolin.cog-uk.io/)
• qc.overallStatus : QC evaluation of sequence. Any alphanumeric string.
• date_prel : date of sampling (DD/MM/YYY)
• DDN : date of birth (YYYY)
• UH : Origin of the patient. Any alphanumeric string.
• nb_labo : Patient codification. Any alphanumeric string.
• sexe : Gender. Any alphanumeric string.
• aaSubstitutions : aminoacid changes (example: N:M234I,ORF1a:D827G,S:D614G). Use one letter AA
• aaDeletions : aminoacid deletions (example: ORF1a:M85-,ORF1a:V86-). Use one letter AA then add in column the annotations you are interested in testing

2]. tree : Alignment tree.newick

Packages needed

The application was built on R version 4.0.2.

The following dependencies are required: shiny (v1.6.0) shinyWidgets (v0.6.0) shinyjs (v2.0.0) tidyverse (v1.3.0) knitr (v1.3.1) ggtree (v2.0.0 not +) tidytree (v0.3.3) treeio (v1.10.0 or +) ggplot2 (v3.3.3) g3viz (v1.1.3 or +) janitor(v2.1.0) lubridate (v1.7.10) rcartocolor (v2.0.0) ggtext (v0.1.1) shadowtext (v0.0.7) forcats (v0.5.1) dplyr (v1.0.3 or +) plotly (v4.9.3)

The tested versions are indicated in brackets

Run the install.R script to install the required packages in the specific versions for ggtree and treeio.

Note: You only need to install those packages once (or not at all, if all these packages are already on your system).

Starting the app

Click "Clone or download" -> "Download ZIP". Find the zip file (typically in your Downloads folder) and extract it to a desired location. Open the app.R file in RStudio and click "Run app".

Contributors

• Sandrine Imbeaud, Dr. PhD, INSERM UMRS1138, Centre de Recherches des Cordeliers - Sorbonne Université-Inserm-Université de Paris, Paris, France

• Wack Maxime, MD, Département d'Informatique Médicale, Biostatistiques et Santé Publique @, HEGP, Paris, France

• Veyer David, PharmaD, PhD, INSERM UMRS1138, Centre de Recherches des Cordeliers - Sorbonne Université-Inserm-Université de Paris, Paris, France Unité de Virologie, Service de Microbiologie, HEGP, Paris, France

• Péré Hélène, PharmaD, PhD, INSERM UMRS1138, Centre de Recherches des Cordeliers - Sorbonne Université-Inserm-Université de Paris, Paris, France Unité de Virologie, Service de Microbiologie, HEGP, Paris, France

License

Copyright (C) 2021 Sandrine Imbeaud

CoV is a free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.