Workflows

What is a Workflow?
Created At
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Updated At
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298 Workflows visible to you, out of a total of 311
Stable

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 ...

Type: KNIME

Creator: Jeanette Reinshagen

Submitter: Jeanette Reinshagen

Stable

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")

Type: KNIME

Creator: Jeanette Reinshagen

Submitter: Jeanette Reinshagen

Stable

BackTrackBB is a program for detection and space-time location of seismic sources based on multi-scale, frequency-selective statistical coherence of the wave field recorded by dense large-scale seismic networks and local antennas. The method is designed to enhance coherence of the signal statistical features across the array of sensors and consists of three steps. They are signal processing, space-time imaging and detection and location.

More information: https://backtrackbb.github.io/

Type: PyCOMPSs

Creators: Natalia Poiata, Claudio Satriano, Javier Conejero

Submitter: Raül Sirvent

Work-in-progress
No description specified

A workflow for marine Genomic Observatories data analysis

An EOSC-Life project

Build Status

The workflows developed in the framework of this project are based on pipeline-v5 of the MGnify resource.

This branch is a child of the pipeline_5.1 branch that contains all CWL descriptions of the MGnify ...

Type: Common Workflow Language

Creators: Haris Zafeiropoulos, Martin Beracochea

Submitter: Haris Zafeiropoulos

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

Stable

StructuralVariants Workflow

Type: Nextflow

Creators: Laura Rodriguez-Navas, Adrián Muñoz-Civico, Daniel López-López

Submitter: Laura Rodriguez-Navas

Work-in-progress

Snakemake workflow: FAIR CRCC - image conversion

Snakemake GitHub actions status

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

Type: Snakemake

Creator: Luca Pireddu

Submitter: Luca Pireddu

Snakemake workflow: dna-seq-varlociraptor

Snakemake GitHub actions status DOI

A ...

Type: Snakemake

Creator: Johannes Köster

Submitter: Johannes Köster

Stable

Fastq-to-BAM @ NCI-Gadi is a genome alignment workflow that takes raw FASTQ files, aligns them to a reference genome and outputs analysis ready BAM files. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel, either massively parallel using the scatter-gather approach or parallel by sample. It consists of a number of stages and follows the BROAD Institute's best practice ...

Type: Shell Script

Creators: Cali Willet, Tracy Chew, Georgina Samaha, Rosemarie Sadsad, Andrey Bliznyuk, Ben Menadue, Rika Kobayashi, Matthew Downton, Yue Sun

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.146.1

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