DFD

Get Drugs From Differential expression profile

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("signatureSearch")
BiocManager::install("signatureSearchData")
install.packages("DFD")

Description

Get Drug information from given differential expression profile. The package search for the bioactive compounds from reference databases such as LINCS containing the genome-wide GESs from tens of thousands of drug and genetic perturbations Subramanian et al. 2017.

Pipeline

• The package process the differential expression profile by converting the gene symbols (Human or Mouse) to entrez ids.
• The processed IDs is the passed to signature search matching the input differential expression to reference differential expression in LINCS database.
• The pacakge search for the perturbagens (Drugs) that are assocaited with matched differential expression
• Re-raking step is performed as a last step in order to prioritize drugs that have the maximum number of targets

Documentation

For the documentation see: DFD Documentation.

Package information

• link to package on CRAN: DFD

Usage

Example

library(DFD)
library(signatureSearch)
perts <- run_pipeline(degs_path = "https://raw.githubusercontent.com/MohmedSoudy/datasharing/master/differential-expression.csv",
                      output_path = getwd())

Sample input and output

• Sample Input
• Sample Output

Output description

column	annottaion
pert	name of the drug
cell	name of the cell-line
type	perturbation type
trend	up or down when reference signature is positively or negatively connected with the query signature, respectively
WTCS	weighted Connectivity Score
WTCS_Pval	nominal p-value of WTCS
WTCS_FDR	false discovery rate of WTCS_Pval
NCS	normalized connectivity score
NCSct	NCS summarized across cell types
N_upset or N_downset	number of genes in the query up or down
t_gn_sym	gene symbols of the corresponding drug targets

Contribution Guidelines

For bugs and suggestions, the most effective way is by raising an issue on the github issue tracker. Github allows you to classify your issues so that we know if it is a bug report, feature request or feedback to the authors.