Description

This method is described in the publication from Biorxiv, 2018 available at [https://www.biorxiv.org/content/10.1101/426593v2]

ICTD web application demo is available at : [https://shiny.ph.iu.edu/ICTD/]

ICTD web application tutorial is available at : [https://github.com/changwn/ICTD/blob/master/vignettes/ICTD_server_tutorial.md]

Backup link: [https://ictd.ccbb.iupui.edu]

ICTD Framework

Installation

#install dependent pkg
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("impute", version = "3.8")
BiocManager::install("GO.db", version = "3.8")
BiocManager::install("sva", version = "3.8")
BiocManager::install("preprocessCore", version = "3.8")

rforge <- "http://r-forge.r-project.org"
install.packages("estimate", repos=rforge, dependencies=TRUE)

#install ICTD
install.packages("devtools")
devtools::install_github("changwn/ICTD")

Note : For old R version which cannot install 'BiocManager', please use below command to install the dependency.

source("https://bioconductor.org/biocLite.R")
biocLite("impute")
biocLite("GO.db")
biocLite("sva")
biocLite("preprocessCore")

rforge <- "http://r-forge.r-project.org"
install.packages("estimate", repos=rforge, dependencies=TRUE)

Example

library(ICTD)

data_bulk = GSE72056_diri_example[[1]]
ictd_result <- ICTD(data_bulk)

#Return value is a list, which the first element is the predicted proportion and 
#the second element is the predicted markers of ICTD

Questions & Problems

If you have any questions or problems when using ICTD, please feel free to open a new issue here. We will fix the new issue ASAP. You can also email the maintainers and authors below.

• Wennan Chang (wnchang@iu.edu)

PhD candidate at BDR group, Indiana University School of Medicine

• Chi Zhang (czhang87@iu.edu)

Assistant Professor

Department of Medical & Molecular Genetics, Indiana University School of Medicine

Dependencies

We also provide a Docker image to recreate the compute environment. See the Dockerfile for more details.

[https://hub.docker.com/r/wnchang/ictd]

Using the Docker image could void the conflict issue that R version and several R packages version confict.

For more details about the Docker, please see Docker documentation page [https://docs.docker.com/].