FUNKI: Interactive functional footprint-based analysis of omics data

09/13/2021
by   Rosa Hernansaiz-Ballesteros, et al.
0

Motivation: Omics data, such as transcriptomics or phosphoproteomics, are broadly used to get a snap-shot 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 signaling 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 several omics data, either from bulk or single-cell experiments. FUNKI also features different options to visualise the results and run post-analyses, and is mirrored as a scripted version in R. Availability: FUNKI is a free and open-source application built on R and Shiny, available in GitHub at https://github.com/saezlab/ShinyFUNKI under GNU v3.0 license and accessible also in https://saezlab.shinyapps.io/funki/ Contact: pub.saez@uni-heidelberg.de Supplementary information: We provide data examples within the app, as well as extensive information about the different variables to select, the results, and the different plots in the help page.

READ FULL TEXT
POST COMMENT

Comments

There are no comments yet.

Authors

page 3

11/03/2020

Brain Predictability toolbox: a Python library for neuroimaging based machine learning

Summary Brain Predictability toolbox (BPt) represents a unified framewor...
12/17/2021

SimPlot++: a Python application for representing sequence similarity and detecting recombination

Motivation: Accurate detection of sequence similarity and homologous rec...
01/28/2021

Peptipedia: a comprehensive database for peptide research supported by Assembled predictive models and Data Mining approaches

Motivation: Peptides have attracted the attention in this century due to...
09/24/2018

Vis-DSS: An Open-Source toolkit for Visual Data Selection and Summarization

With increasing amounts of visual data being created in the form of vide...
03/17/2021

TNM: A Tool for Mining of Socio-Technical Data from Git Repositories

Networks of collaboration between engineers are reflected in traces of d...
11/11/2020

FastPathology: An open-source platform for deep learning-based research and decision support in digital pathology

Deep convolutional neural networks (CNNs) are the current state-of-the-a...
03/06/2017

Cellulyzer - Automated analysis and interactive visualization/simulation of select cellular processes

Here we report on a set of programs developed at the ZMBH Bio-Imaging Fa...
This week in AI

Get the week's most popular data science and artificial intelligence research sent straight to your inbox every Saturday.