Workflows

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831 Workflows visible to you, out of a total of 904
EJP-RD WP13 case-study: CAKUT peptidome and miRNome data analysis using the DIABLO and PLS-DA methods from the mixOmics R package
Stable

For integrative analysis of CAKUT multi-omics data DIABLO method of the mixOmics package (version 6.10.9. Singh et. al. 2019) was used with sPLS-DA (sparse Partial Least Squares Discriminant Analysis Discriminant Analysis) and PLS-DA classification.

Type: Snakemake

Creators: Juma Bayjan, Ozan Ozisik, Cenna Doornbos, Friederike Ehrhart

Submitter: Juma Bayjan

EJP-RD WP13 case-study: CAKUT proteome, peptidome and miRNome data analysis using WikiPathways
Stable

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 ...

Type: Snakemake

Creators: Woosub Shin, Friederike Ehrhart, Juma Bayjan, Cenna Doornbos, Ozan Ozisik

Submitter: Juma Bayjan

PacBio HiFi genome assembly using hifiasm v2.1
Stable

PacBio HiFi genome assembly using hifiasm v2.1

General usage recommendations

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

See change log

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian ...

Type: Galaxy

Creators: Gareth Price, Katherine Farquharson

Submitter: Johan Gustafsson

DOI: 10.48546/workflowhub.workflow.221.3

Purge duplicates from hifiasm assembly v1.0
Stable

Purge-duplicates-from-hifiasm-assembly

General recommendations for using Purge-duplicates-from-hifiasm-assembly

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian ...

Type: Galaxy

Creators: Gareth Price, Gareth Price

Submitter: Johan Gustafsson

DOI: 10.48546/workflowhub.workflow.237.2

BAM to FASTQ + QC v1.0
Stable

BAM-to-FASTQ-QC

General recommendations for using BAM-to-FASTQ-QC

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian Research Data Commons (https://doi.org/10.47486/PL105) ...

Type: Galaxy

Creator: Gareth Price

Submitter: Johan Gustafsson

DOI: 10.48546/workflowhub.workflow.220.2

ChIPseq_PE/main

ChIP-seq paired-end Workflow

Inputs dataset

  • The workflow needs a single input which is a list of dataset pairs of fastqsanger.

Inputs values

  • adapters sequences: this depends on the library preparation. If you don't know, use FastQC to determine if it is Truseq or Nextera.
  • reference_genome: this field will be adapted to the genomes available for bowtie2.
  • effective_genome_size: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes).

...

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

IndexReferenceFasta-nf
Stable

IndexReferenceFasta-nf

===========

Type: Nextflow

Creator: Georgina Samaha

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.393.1

DRC_cellbased_OutlierDetection
Stable

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 ...

Type: KNIME

Creator: Jeanette Reinshagen

Submitter: Jeanette Reinshagen

DRC_biochemical_toECBD
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

DRC_template_toxicity
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

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