Workflows

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747 Workflows visible to you, out of a total of 808
Ecoregionalization workflow (Part 2)

Second part of the ecoregionalization

This workflow allows you to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.

The workflow is intended for processing occurrence data, which should include latitude, longitude and species presence or absence. You can use example test data available with the workflow, highlighting a use case centered on the Dumont d'Urville sea region and benthic invertebrates. The primary goal of ...

Type: Galaxy

Creator: Pauline Seguineau

Submitter: Pauline Seguineau

DOI: 10.48546/workflowhub.workflow.1209.1

Ecoregionalization workflow (Part 1)

Part 1 of ecoregionalization workflow

This workflow allows you to create an ecoregionalization map from occurrences and environmental data using a boosted regression trees model for predictions.

The workflow is intended for processing occurrence data, which should include latitude, longitude and species presence or absence. You can use example test data available with the workflow, highlighting a use case centered on the Dumont d'Urville sea region and benthic invertebrates. The primary goal of ...

Type: Galaxy

Creator: Pauline Seguineau

Submitter: Pauline Seguineau

DOI: 10.48546/workflowhub.workflow.1208.1

Fgenesh annotation -TSI

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

Inputs required: assembled-genome.fasta, hard-repeat-masked-genome.fasta, and (because this workflow maps known mRNA ...

Type: Galaxy

Creator: Luke Silver

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.881.5

pseudobulk-worflow-decoupler-edger/main

This workflow uses the decoupler tool in Galaxy to generate pseudobulk counts from an annotated AnnData file obtained from scRNA-seq analysis. Following the pseudobulk step, differential expression genes (DEG) are calculated using the edgeR tool. The workflow also includes data sanitation steps to ensure smooth operation of edgeR and minimizing potential issues. Additionally, a Volcano plot tool is used to visualize the results after the DEG analysis.

Type: Galaxy

Creators: Diana Chiang Jurado, Pavankumar Videm, Pablo Moreno

Submitter: WorkflowHub Bot

Proximity interactomes of human PRICKLE1, PRICKLE2 and PRICKLE3.

KNIME workflow describing the analysis of mass spectrometry dataset related to the publication "Armed with PRICKLE(3)s: Stabilizing WNT/PCP complexes against RNF43-mediated ubiquitination". Workflow was built using the KNIME software container environment, version 4.7.7a, which can be created using "docker pull cfprot/knime:4.7.7a" command in Docker. The input data for the KNIME workflow (the report.tsv from DIA-NN) can be found on PRIDE repository under the identifier PXD057854.

Type: KNIME

Creators: Kristina Gomoryova, David Potěšil

Submitter: Kristina Gomoryova

DOI: 10.48546/workflowhub.workflow.1202.1

GALOP - Genome Assembly using Long reads Pipeline
Work-in-progress

GALOP - Genome Assembly using Long reads Pipeline

This repository contains an exact copy of the standard Genoscope long reads assembly pipeline.

At the moment, this is not intended for users to download as it uses grid submission commands that will only work at Genoscope. As time goes on, we intend to make this pipeline available to a broader audience. However, genome assembly and polishing commands are accessible in the lib/assembly.py and lib/polishing.py files.

galop.py -h 
Mandatory
...

Type: Python

Creators: Benjamin Istace, Jean-Marc Aury, Caroline Belser

Submitter: Benjamin Istace

DOI: 10.48546/workflowhub.workflow.1200.2

rnaseq-de/main

This workflow can only work on an experimental setup with exactly 2 conditions. It takes two collections of count tables as input and performs differential expression analysis. Additionally it filters for DE genes based on adjusted p-value and log2 fold changes thresholds. It also generates informative plots.

Type: Galaxy

Creator: Pavankumar Videm

Submitter: WorkflowHub Bot

cfDNA UniFlow: A unified preprocessing pipeline for cell-free DNA data from liquid biopsies
Stable

cfDNA UniFlow is a unified, standardized, and ready-to-use workflow for processing whole genome sequencing (WGS) cfDNA samples from liquid biopsies. It includes essential steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Finally, we provide specialized methods for extracting coverage derived signals and visualizations comparing cases and controls. ...

Type: Snakemake

Creator: Sebastian Röner

Submitter: Sebastian Röner

DOI: 10.48546/workflowhub.workflow.1091.2

goseq/main

This workflow is used for GO and KEGG enrichment analysis using GOseq tools.

Type: Galaxy

Creator: Amirhossein Naghsh Nilchi

Submitter: WorkflowHub Bot

Multiomic ALS signatures highlight sex differences and molecular subclusters and identify the MAPK pathway as therapeutic target
Stable

This repository contains the analytical pipeline for the MAXOMOD project, which focuses on the multi-omic analysis of axono-synaptic degeneration in the motor neuron disease amyotrophic lateral sclerosis (ALS). The project explores sex differences and molecular subclusters in ALS and investigates the MAPK pathway as a potential therapeutic target.

For a detailed understanding of the scientific background and the findings, refer to our paper published on [Nature ...

Type: DVC

Creator: Fabian Hausmann

Submitter: Fabian Hausmann

DOI: 10.48546/workflowhub.workflow.1191.1

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