renjun0324 / ti_dbcti

A docker container for dbcti, mainly for cell trajectory inference analysis of single cell RNA-seq data

ti_dbcti

A docker container for dbcti, mainly for cell trajectory inference analysis of single cell RNA-seq data

dbcti repository

https://github.com/tianlt/dbcti

pull container

docker pull renjun0324/ti_dbcti

quick start

library(dynwrap)
library(dynmethods)
library(dyntoy)
library(tidyverse)
library(purrr)
library(dyno)

data("fibroblast_reprogramming_treutlein")

dataset <- wrap_expression(
  counts = fibroblast_reprogramming_treutlein$counts,
  expression = fibroblast_reprogramming_treutlein$expression
)
                               
ti_dbcti = create_ti_method_container("renjun0324/ti_dbcti")
model = infer_trajectories(dataset_wrap, ti_dbcti(), 
                             verbose = TRUE, return_verbose = TRUE, debug = FALSE)
model$model = map(model$model, add_cell_waypoints)
metric <- map_dfr(model$model,
                  dyneval::calculate_metrics,
                  dataset = dataset,
                  metrics = c("featureimp_wcor", "him",  "F1_branches", "correlation"))