Dataset Information
FUNKI: interactive functional footprint-based analysis of omics data.
Ontology highlight
ABSTRACT: Motivation
Omics data are broadly used to get a snapshot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription factors and kinases based on known regulated targets, that we call footprints. Then the molecular paths driving these activities can be estimated using causal reasoning on large signalling networks.Results
We have developed FUNKI, a FUNctional toolKIt for footprint analysis. It provides a user-friendly interface for an easy and fast analysis of transcriptomics, phosphoproteomics and metabolomics data, either from bulk or single-cell experiments. FUNKI also features different options to visualize the results and run post-analyses, and is mirrored as a scripted version in R.Availability and implementation
FUNKI is a free and open-source application built on R and Shiny, available at https://github.com/saezlab/ShinyFUNKI and https://saezlab.shinyapps.io/funki/.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Hernansaiz-Ballesteros R
PROVIDER: S-EPMC8963329 | biostudies-literature | 2022 Mar
REPOSITORIES: biostudies-literature
Publications
FUNKI: interactive functional footprint-based analysis of omics data.
Bioinformatics (Oxford, England) 20220301 7
<h4>Motivation</h4>Omics data are broadly used to get a snapshot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription factors and kinases based on known regulated targets, that we call footprints. Then the molecular paths driving these activities can be estimated using causal reasoning on large signalling networks.<h4>Results</h4>We have developed FUNKI, a FUNctional toolKIt for footprint analysis. It provides a user-fr ...[more]