In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics datasets. For this, each of the three -omics datasets was first analyzed to identify differentially expressed elements, and pathways associated with the significant miRNA-protein links were detected. A miRNA-protein link is deemed significant, and may possibly be implying causality, if both a miRNA and its target are significantly differentially expressed.

The peptidome and ...

This workflow can be used to fit dose-response curves from normalised cell-based assay data (%confluence) using the KNIME HCS extension. The workflow expects triplicates for each of eight test concentrations. This workflow needs R-Server to run in the back-end. Start R and run the following command: library(Rserve); Rserve(args = "--vanilla"). Three types of outliers can be removed: 1 - Outliers from triplicate measurement (standard deviation cut-off can be selected), 2 - inactive and weekly ...

This workflow can be used to fit dose-response curves from normalised biochemical assay data (%Inhibition) using the HCS extension. This workflow needs R-Server to run in the back-end. Start R and run the following command: library(Rserve); Rserve(args = "--vanilla") IC50 values will not be extrapolated outside the tested concentration range For activity classification the following criteria are applied:

• maximum (average % inhibion) >25 % and slope is >0 and IC50 > 5 µM or
• minimum ...

Generates Dose-response curve fits on cell-based toxicity data. Outliers of replicate data-sets can be removed by setting a threshold for standard deviation (here set to 25). Curve fits for compounds showing low response can be removed by setting a threshold for minimum activity (here set to 75% confluence). This workflow needs R-Server to run in the back-end. Start R and run the following command: library(Rserve); Rserve(args = "--vanilla")

StructuralVariants Workflow

Snakemake workflow: FAIR CRCC - image conversion

A Snakemake workflow for converting whole-slide images (WSI) from the CRC Cohort ...

Snakemake workflow: dna-seq-varlociraptor

A ...

A prototype implementation of the Air Quality Prediction pipeline in Galaxy, using CWL tools.

ABR_Threshold_Detection

What is this?

This code can be used to automatically determine hearing thresholds from ABR hearing curves.

One of the following methods can be used for this purpose:

• neural network (NN) training,
• calibration of a self-supervised sound level regression (SLR) method

on given data sets with manually determined hearing thresholds.

Installation:

Run inside the src directory:

Installation as python package

pip install -e ./src (Installation as python
...