Workflows

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817 Workflows visible to you, out of a total of 891
Workflow 2: Sciensano
database database version
ResFinder 2022-07-19
CARD 2023-12-03

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

Workflow 4: Staramr
Work-in-progress

Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr.

Doi: 10.3390/microorganisms10020292

tool version license
staramr 0.8.0 Apache-2.0 license

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

Workflow 1: AbritAMR
tool version license
abritAMR 1.0.14 CC-BY-4.0

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

GADES reproducibility workflow
Stable

Article-GADES

This repository represents generating and benchmarking the results of the GADES package for Distance Matrix Calculation

Installation

git lfs install 
git clone https://github.com/lab-medvedeva/Article-GADES.git 
cd Article-GADES

Put the Real datasets in the MEX format to the folder Datasets/Real.

Running benchmark using Docker Deployment

docker run --gpus all \ 
-v $PWD/Datasets:/workspace/Article-GADES/Datasets
...

Type: Docker

Creator: Pavel Akhtyamov

Submitter: Pavel Akhtyamov

DOI: 10.48546/workflowhub.workflow.1125.1

PhysioNet CascadeSVM Kfold

Name: PhysioNet CascadeCSVM Kfold Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

Kfold to evaluate CascadeCSVM accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0

Type: COMPSs

Creator: Fernando Vázquez-Novoa

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.1124.1

PhysioNet RF Kfold

Name: PhysioNet RF Kfold Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

Kfold to evaluate RandomForest accuracy on PhysioNet dataset (https://b2drop.bsc.es/index.php/s/8Q8MefXX2rrzaWs). This application used dislib-0.9.0

Type: COMPSs

Creator: Fernando Vázquez-Novoa

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.1122.1

Genome assembly workflow for nanopore reads, for TSI

Genome assembly workflow for nanopore reads, for TSI

Input:

  • Nanopore reads (can be in format: fastq, fastq.gz, fastqsanger, or fastqsanger.gz)

Optional settings to specify when the workflow is run:

  • [1] how many input files to split the original input into (to speed up the workflow). default = 0. example: set to 2000 to split a 60 GB read file into 2000 files of ~ 30 MB.
  • [2] filtering: min average read quality score. default = 10
  • [3] filtering: min read length. default = 200
  • [4] ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.1114.1

Full Analyse Argo data

Process argo data with the Pangeo Ecosystem and visualise them with Ocean Data View (ODV)

Type: Galaxy

Creator: Marie Jossé

Submitter: Marie Jossé

Workflow for differential expression analysis in proteomics data and overlaying DEPs on COVID-19 Disease Map

A R workflow for proteomics data analysis is reported. This pipeline was basing on protein expression projects, stored on the PRIDE database and reported on the COVID-19 Data portal. This is an R pipeline to analyze protein expression data, built on lung cell lines infected by SARS-CoV-2 variants: ​B.1, Delta, and Omicron BA.1 (Mezler et al. 2023) https://www.ebi.ac.uk/pride/archive/projects/PXD037265. This pipeline can obtain DEPs for each variant, starting from normalized protein expression ...

Type: R markdown

Creator: Francesco Messina

Submitter: Francesco Messina

Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning
Stable

GraphRBF is a state-of-the-art protein-protein/nucleic acid interaction site prediction model built by enhanced graph neural networks and prioritized radial basis function neural networks. This project serves users to use our software to directly predict protein binding sites or train our model on a new database. Identification of protein-protein and protein-nucleic acid binding sites provides insights into biological processes related to protein functions and technical guidance for disease ...

Type: BioCompute Object

Creator: 仕卓 张

Submitter: 仕卓 张

DOI: 10.48546/workflowhub.workflow.1107.1

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