meisamysf / generamen

Gene Rank Meta aNalyzer (GeneRaMeN) is an R/Shiny app for integration, comparison, and meta analysis of multiple ranked gene lists, presented in Yousefi et al. (2024) Briefings in bioinformatics.

GeneRaMeN

Gene Rank Meta aNalyzer (GeneRaMeN) is an R/Shiny app designed for integration, comparison, and meta analysis of multiple ranked gene lists, with a primary focus on genome-wide CRISPR screening outputs. GeneRaMeN consists of three main functionalities:

1. Rank aggregation: It enables the user to combine multiple ranked gene lists into one consensus list, using rank aggregation algorithms like RRA. It brings us what is homogenous across our datasets.

2. Rank uniqueness: It enables the user to compare a subset of the ranked gene lists with the rest, basically using rank aggregation algorithms on each of the subsets and then comparing them with eachother. It brings us what is heterogenous across our datasets.

3. Rank correlation: It enables the user to observe correlation/anti-correlations in gene ranks, finding genes that show a similar or opposite trend with a gene of interest.

GeneRaMeN can be accessed on our shinyapps web server, or be downloaded from here and run locally.