Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Antarctic sea ecoregionalization" .

This workflow allows to analyze marine benthic biodiversity data to compute ecoregions regarding environmental data.

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Sentinel 2 biodiversity" .

This workflow allows to analyze remote sensing sentinel 2 satellites data to compute spectral indices such as the NDVI and visualizing biodiversity indicators

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Biodiversity data exploration"

This workflow allows to explore biodiversity data looking at homoscedasticity, normality or collinearity of presences-absence or abundance data and at comparing beta diversity taking into account space, time and species components ...

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Metabarcoding/eDNA through Obitools" .

This workflow allows to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools.

Autosubmit mHM test domains

A variation of the Cancer variant annotation (hg38 VEP-based) workflow at https://doi.org/10.48546/workflowhub.workflow.607.1.

Like that other workflow it takes a list of tumor/normal sample pair variants in VCF format (see the other workflow for details about the expected format) and

1. annotates them using the ENSEMBL Variant Effect Predictor and custom annotation data
2. turns the annotated VCF into a MAF file for import into cBioPortal
3. generates human-readable variant- and gene-centric ...

Call somatic, germline and LoH event variants from PE Illumina sequencing data obtained from matched pairs of tumor and normal tissue samples.

This workflow can be used with whole-genome and whole-exome sequencing data as input. For WES data, parts of the analysis can be restricted to the exome capture kits target regions by providing the optional "Regions of Interest" bed dataset.

The current version uses bwa-mem for read mapping and varscan somatic for variant calling and somatic status ...

MMV Im2Im Transformation

A generic python package for deep learning based image-to-image transformation in biomedical applications

The main branch will be further developed in order to be able to use the latest state of the art techniques and methods in the future. To reproduce the results of our manuscript, we refer to the branch ...

rquest-omop-worker-workflows

Source for workflow definitions for the open source RQuest OMOP Worker tool developed for Hutch/TRE-FX

Note: ARM workflows are currently broken. x86 ones work.

Inputs

### Body Sample input payload:

{ 
"task_id": "job-2023-01-13-14: 20: 38-", 
"project": "", 
"owner": "", 
"cohort": { 
"groups": [ 
{ 
"rules": [ 
{ 
"varname": "OMOP", 
"varcat": "Person", 
"type": "TEXT", 
"oper": "=", 
"value": "8507" 
} 
], 
"rules_oper": "AND" 
} 
], 
"groups_oper": "OR" 
}, 
"collection":
...

Summary

The data preparation pipeline contains tasks for two distinct scenarios: leukaemia that contains microarray data for 119 patients and ovarian cancer that contains next generation sequencing data for 380 patients.

The disease outcome prediction pipeline offers two strategies for this task:

Graph kernel method: It starts generating personalized networks for ...