BACteria COmmunicatioN (BACON), a method that utilizes single-microbe RNA sequencing data to infer, visualize and analyze quorum sensing on single species and human gut microbiome.
You can install the latest version of BACON like so:
devtools::install_github("qu-wx/BACON")library(BACON)
## create BACON object
example_BACON_object <- createBACON(object = as.matrix(gene_count_matrix),group.by = metadata$select_vector,database = database)
## calculation of quorum sensing networks
example_BACON_object <- run_BACON(object = example_BACON_object,M=100)
## aggregating the network
qs_aggregated <- net_aggregation(example_BACON_object@net)
## visulization
netVisual_circle_BACON(example_BACON_object@net$select_qs)Database construction for cross-species
Inference and visualization of quorum sensing network
R >= 4.1.0
dplyr >= 1.0.9
data.table >= 1.14.2
Seurat >= 4.1.0
SeuratObject >= 4.1.0
igraph >= 1.3.4
ggplot2 >= 3.3.6
ComplexHeatmap >= 2.8.0
circlize >= 0.4.14
ggalluvial >= 0.12.3 