Description

The workflow takes an input file with Cancer Driver Genes predictions (i.e. the results provided by a participant), computes a set of metrics, and compares them against the data currently stored in OpenEBench within the TCGA community. Two assessment metrics are provided for that predictions. Also, some plots (which are optional) that allow to visualize the performance of the tool are generated. The workflow consists in three standard steps, defined by OpenEBench. The tools needed ...

Summary

This notebook shows how to integrate genomic and image data resources. This notebook looks at the question Which diabetes related genes are expressed in the pancreas?

Steps:

• Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the genes.
• Using the list of found genes, search in the Image Data Resource (IDR) for images linked to the genes, tissue and disease.

We use the intermine API and the IDR API

The notebook can be launched ...

atavide is a complete workflow for metagenomics data analysis, including QC/QA, optional host removal, assembly and cross-assembly, and individual read based annotations. We have also built in some advanced analytics including tools to assign annotations from reads to contigs, and to generate metagenome-assembled genomes in several different ways, giving you the power to explore your data!

atavide is 100% snakemake and conda, so you only need to install the snakemake workflow, and then ...

Exome SAMtools Workflow

Exome Alignment Workflow

Summary

This notebook demonstrates how to retrieve metadata associated to the paper A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection and available in IDR at idr0094-ellinger-sarscov2. Over 300 compounds were used in this investigation. This notebook allows the user to calculate the half maximal inhibitory concentration (IC50) for ...

This notebook is about pre-processing the Auditory Brainstem Response (ABR) raw data files provided by Ingham et. al to create a data set for Deep Learning models.

The unprocessed ABR data files are available at Dryad.

Since the ABR raw data are available as zip-archives, these have to be unzipped and the extracted raw data files parsed so that the time ...

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps:

• FastQC (read quality control)
• NGTax 2.0
• Picrust 2
• Export module for ngtax

Analysis of RNA-seq data starting from BAM and focusing on mRNA, lncRNA and miRNA

This workflow is based on the idea of comparing different gene sets through their semantic interpretation. In many cases, the user studies a specific phenotype (e.g. disease) by analyzing lists of genes resulting from different samples or patients. Their pathway analysis could result in different semantic networks, revealing mechanistic and phenotypic divergence between these gene sets. The workflow of BioTranslator Comparative Analysis compares quantitatively the outputs of pathway analysis, ...