The goal of microbialpanels is to provide curated lists of microbes relevant to specific applications
You can install the development version of microbialpanels like so:
# install.packages("remotes") # Install remotes package if you haven't already got it
remotes::install_github("CCICB/microbialpanels")
library(microbialpanels)
# List available panels
panels_available()
#> [1] "HumanMicrobiomeLarge" "OralMicrobiome"
#> [3] "CancerViruses" "CommonNosocomial"
#> [5] "FungalPathogens" "TorqueTenoVirusesSpecies"
#> [7] "TorqueTenoVirusesGenus"
# Load a panel of interest
panels_load('CancerViruses')
#> # A tibble: 15 × 7
#> ScientificName `Common Name` Type Taxid Rank Notes Source
#> <chr> <chr> <chr> <dbl> <chr> <chr> <chr>
#> 1 Human gammaherpesvirus 8 Kaposi's sarc… dsDNA 3.73e4 spec… <NA> https…
#> 2 Human gammaherpesvirus 4 Epstein-Barr … dsDNA 1.04e4 spec… <NA> https…
#> 3 Human betaherpesvirus 6A Herpesvirus t… dsDNA 3.26e4 spec… <NA> https…
#> 4 Human betaherpesvirus 6B Herpesvirus t… dsDNA 3.26e4 spec… <NA> https…
#> 5 Human betaherpesvirus 7 HHV-7 dsDNA 1.04e4 spec… Not … <NA>
#> 6 Primate T-lymphotropic virus 1 <NA> retr… 1.94e5 spec… <NA> https…
#> 7 Human papillomavirus Human papillo… dsDNA 1.06e4 spec… <NA> https…
#> 8 Hepatitis B virus HBV part… 1.04e4 spec… <NA> https…
#> 9 Hepacivirus C Hepatitis C V… ssRNA 1.11e4 spec… <NA> https…
#> 10 Merkel cell polyomavirus <NA> dsDNA 4.94e5 no r… <NA> https…
#> 11 Betapolyomavirus macacae Simian virus … dsDNA 1.89e6 spec… <NA> https…
#> 12 Betapolyomavirus secuhominis Human polyoma… dsDNA 1.89e6 spec… <NA> https…
#> 13 Betapolyomavirus hominis BK virus dsDNA 1.89e6 spec… <NA> https…
#> 14 Cytolomegalovirus <NA> dsDNA 1.04e4 genus <NA> https…
#> 15 Alphatorquevirus <NA> ssDNA 6.87e5 genus Mark… https…
All panels have the following columns:
-
ScientificName
-
Taxid
-
Type
-
Rank
Panel tables may have additional columns that vary from one panel to another