In krishan57gupta/iCTC: Identification of CTC in Blood Streams

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)

iCTC: identification of circulating tumor cells

The goal of iCTC is to detect whether peripheral blood cells have CTCs (circulating tumor cell) or not.

Installation

The developer version of the R package can be installed with the following R commands:

library(devtools)
install_github("immunogenomics/harmony")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install('iCTC')

or can be installed with the following R commands:

library(devtools)
install_github("immunogenomics/harmony")
install_github('krishan57gupta/iCTC')

Vignette tutorial

This vignette uses a small dataset of cell samples, which is saved in package itself, to demonstrate a standard pipeline. This vignette can be used as a tutorial as well.

Libraries need to be loaded before running iCTC.

library(iCTC)

cell_samples<-iCTC::raw_test_data$Clearcell_Polaris_sample_test
head(cell_samples)

results<-iCTC(cell_samples=cell_samples, cases = c(4,5,6))

results$CTC_probabilistic_score

krishan57gupta/iCTC documentation built on Dec. 31, 2022, 12:33 p.m.