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
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 filevirus
: name of the virus. Any alphanumeric string. Default="sars_cov_2clade
: 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 AAaaDeletions
: 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
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).
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".
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Sandrine Imbeaud, Dr. PhD, INSERM UMRS1138, Centre de Recherches des Cordeliers - Sorbonne Université-Inserm-Université de Paris, Paris, France
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Wack Maxime, MD, Département d'Informatique Médicale, Biostatistiques et Santé Publique @, HEGP, Paris, France
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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
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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
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 https://www.gnu.org/licenses/.