The goal of syncons is to support massive construction of synthetic
communities (SynComs) with 24-, 96- and 384-well plates.
Installation
You can install the development version of syncons like so:
install.packages("pak") pak::pak("gaospecial/syncons")
Now you can use this package.
library("syncons")A shiny app ported with this package can be accessed through shiny.io.
Screenshot of the shiny
app
Layout of SynComs in a plate
A 24-well plate can be used to construct 16 different SynComs with 4 strains.
one_plate(24, return_layout = TRUE) #> # A tibble: 4 × 5 #> row `1` `2` `3` `4` #> <chr> <chr> <chr> <chr> <chr> #> 1 A S1/S2/S3/S4 S1/S3/S4 S2/S3/S4 "S3/S4" #> 2 B S1/S2/S3 S1/S3 S2/S3 "S3" #> 3 C S1/S2/S4 S1/S4 S2/S4 "S4" #> 4 D S1/S2 S1 S2 ""
A 96-well plate can be used to construct 64 different SynComs with 6 strains.
one_plate(96, return_layout = TRUE) #> # A tibble: 8 × 9 #> row `1` `2` `3` `4` `5` `6` `7` `8` #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 A S1/S2/S3/S4/S5/S6 S1/S2/S4/S5/S6 S1/S3/S4… S1/S… S2/S… S2/S… S3/S… "S4/… #> 2 B S1/S2/S3/S4/S5 S1/S2/S4/S5 S1/S3/S4… S1/S… S2/S… S2/S… S3/S… "S4/… #> 3 C S1/S2/S3/S4/S6 S1/S2/S4/S6 S1/S3/S4… S1/S… S2/S… S2/S… S3/S… "S4/… #> 4 D S1/S2/S3/S4 S1/S2/S4 S1/S3/S4 S1/S4 S2/S… S2/S4 S3/S4 "S4" #> 5 E S1/S2/S3/S5/S6 S1/S2/S5/S6 S1/S3/S5… S1/S… S2/S… S2/S… S3/S… "S5/… #> 6 F S1/S2/S3/S5 S1/S2/S5 S1/S3/S5 S1/S5 S2/S… S2/S5 S3/S5 "S5" #> 7 G S1/S2/S3/S6 S1/S2/S6 S1/S3/S6 S1/S6 S2/S… S2/S6 S3/S6 "S6" #> 8 H S1/S2/S3 S1/S2 S1/S3 S1 S2/S3 S2 S3 ""
A 384-well plate can be used to construct 256 different SynComs with 8 strains.
one_plate(384, return_layout = TRUE) #> # A tibble: 16 × 17 #> row `1` `2` `3` `4` `5` `6` `7` `8` `9` `10` `11` `12` #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 A S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 2 B S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 3 C S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 4 D S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 5 E S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 6 F S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 7 G S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 8 H S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S5 S2/S… S2/S… S2/S… S2/S5 #> 9 I S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 10 J S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 11 K S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 12 L S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S6 S2/S… S2/S… S2/S… S2/S6 #> 13 M S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S2/S… S2/S… S2/S… S2/S… #> 14 N S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S7 S2/S… S2/S… S2/S… S2/S7 #> 15 O S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S… S1/S8 S2/S… S2/S… S2/S… S2/S8 #> 16 P S1/S… S1/S… S1/S… S1/S2 S1/S… S1/S3 S1/S4 S1 S2/S… S2/S3 S2/S4 S2 #> # ℹ 4 more variables: `13` <chr>, `14` <chr>, `15` <chr>, `16` <chr>
Generation of sample tables
Support we have eight strains and want to construct a series of SynComs with all the possible combinations.
strains = paste0("S", 1:8) assign_plate(strains, plate_type = "96") #> # A tibble: 256 × 2 #> combination_id combination #> <chr> <chr> #> 1 P1A1 S1/S2/S3/S4/S5/S6 #> 2 P1B1 S1/S2/S3/S4/S5 #> 3 P1C1 S1/S2/S3/S4/S6 #> 4 P1D1 S1/S2/S3/S4 #> 5 P1E1 S1/S2/S3/S5/S6 #> 6 P1F1 S1/S2/S3/S5 #> 7 P1G1 S1/S2/S3/S6 #> 8 P1H1 S1/S2/S3 #> 9 P1A2 S1/S2/S4/S5/S6 #> 10 P1B2 S1/S2/S4/S5 #> # ℹ 246 more rows
Generation of supplementary information
This is for Bio-Protocol submission.
strains = paste0("S", 1:11) sheets = list( sheet1 = assign_plate(strains[1:4]), sheet2 = assign_plate(strains[1:5]), sheet3 = assign_plate(strains[1:6], plate_type = "96"), sheet4 = assign_plate(strains[1:7], plate_type = "96"), sheet5_1 = assign_plate(strains[1:8], plate_type = "96"), sheet5_2 = assign_plate(strains[1:8], plate_type = "384"), sheet6_1 = assign_plate(strains[1:9], plate_type = "96"), sheet6_2 = assign_plate(strains[1:9], plate_type = "384"), sheet7 = assign_plate(strains[1:10], plate_type = "384"), sheet8 = assign_plate(strains[1:11], plate_type = "384") ) openxlsx::write.xlsx(sheets, file = "Sheets.xlsx")