iSEEfier: Starting to use iSEE became even easier

Author(s): Najla Abassi,Federico Marini

Affiliation(s): Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany



Effectively exploring and visualizing omics data is one paramount step for uncovering new biological insights. A variety of software solutions have been developed for this end, among them iSEE, which is a tool that can be implemented for various purposes at any stage of the data analysis pipeline. However, its flexibility and the diversity of its features can be overwhelming for new users seeking different, yet basic/foundational visualization goals. To streamline this process, we introduced iSEEfier, an R package designed to simplify the task of initializing iSEE exploration sessions on single-cell RNA-seq, bulk RNA-seq, and proteomics data. Using iSEEinit, iSEEfier can initiate in a single step a personalized iSEE instance with specific configurations aiming to illustrate the expression of a list of genes, focusing on relevant experimental covariates, without the need to manually and repeatedly setting up individual panels inside the App. Previewing the configuration of panels and their layout in a graphical manner can help users to anticipate and understand the content of their iSEE instance. Moreover, iSEEfier can accommodate the usage of custom panels (e.g. included in iSEEu and other companion packages), allowing users to expand its functionality to suit diverse visualization goals and experimental setups. iSEEfier is available on Bioconductor since its latest release at https://www.bioconductor.org/packages/iSEEfier.