Get Drugs From Differential expression profile
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("signatureSearch")
BiocManager::install("signatureSearchData")
install.packages("DFD")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.
- 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
For the documentation see: DFD Documentation.
- link to package on CRAN: DFD
Example
library(DFD)
library(signatureSearch)
perts <- run_pipeline(degs_path = "https://raw.githubusercontent.com/MohmedSoudy/datasharing/master/differential-expression.csv",
output_path = getwd())| 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 |
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.