Workflows

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738 Workflows visible to you, out of a total of 793
BioDT Cultural Ecosystem Services prototype Digital Twin - Recreation Potential Component
Work-in-progress

This is the workflow for the recreation potential component of the cultural ecosystems digital twin

Type: Shell Script

Creators: Chris Andrews, Will Bolton, Simon Rolph, Dylan Carbone, Jan Dick

Submitter: Simon Rolph

Training a CNN model for classification of transcriptional subtypes and survival prediction in glioblastoma
Work-in-progress

GBMatch_CNN

Work in progress... Predicting TS & risk from glioblastoma whole slide images

Reference

Upcoming paper: stay tuned...

Dependencies

python 3.7.7

randaugment by Khrystyna Faryna: https://github.com/tovaroe/pathology-he-auto-augment

tensorflow 2.1.0

scikit-survival 0.13.1

pandas 1.0.3

lifelines 0.25.0

Description

The pipeline implemented here predicts transcriptional subtypes and survival of glioblastoma patients based on H&E stained whole slide scans. Sample data is ...

Type: Python

Creator: Thomas Roetzer-Pejrimovsky

Submitter: Thomas Roetzer-Pejrimovsky

DOI: 10.48546/workflowhub.workflow.883.1

Hecatomb
Stable

A hecatomb is a great sacrifice or an extensive loss. Heactomb the software empowers an analyst to make data driven decisions to 'sacrifice' false-positive viral reads from metagenomes to enrich for true-positive viral reads. This process frequently results in a great loss of suspected viral sequences / contigs.

For information about installation, usage, tutorial etc please refer to the documentation: https://hecatomb.readthedocs.io/en/latest/

Quick start guide

Install Hecatomb from Bioconda ...

Type: Snakemake

Creators: Michael Roach, Scott Handley, Rob Edwards

Submitter: Michael Roach

DOI: 10.48546/workflowhub.workflow.235.1

Download
Convert formats - 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

About this workflow:

  • Inputs: transdecoder-peptides.fasta, transdecoder-nucleotides.fasta
  • Runs many steps ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.880.1

Extract transcripts - 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

About this workflow:

  • Input: merged_transcriptomes.fasta.
  • Runs TransDecoder to produce longest_transcripts.fasta ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.879.1

Combine transcripts - 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

About this workflow:

  • Inputs: multiple transcriptome.gtfs from different tissues, genome.fasta, coding_seqs.fasta, ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.878.1

Find transcripts - 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

About this workflow:

  • Run this workflow per tissue.
  • Inputs: masked_genome.fasta and the trimmed RNAseq reads ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.877.1

QC and trimming of RNAseq reads - 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

About this workflow:

  • Repeat this workflow separately for datasets from different tissues.
  • Inputs = collections ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.876.1

JAX NGS Operations Nextflow DSL2 Pipelines
Stable

DOI

JAX NGS Operations Nextflow DSL2 Pipelines

This repository contains production bioinformatic analysis pipelines for a variety of bulk 'omics data analysis. Please see the Wiki documentation associated with this repository for all documentation and available analysis workflows.

Type: Nextflow

Creators: Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Ardian Ferraj, Anuj Srivastava

Submitter: Michael Lloyd

DOI: 10.48546/workflowhub.workflow.874.1

Tango: Numerical reconciliation of bacterial fermentation in cheese production
Stable

Complete workflow for TANGO as reported in Lecomte et al (2024), "Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling", Metabolic Eng. 83:24-38 https://doi.org/10.1016/j.ymben.2024.02.014

  1. Parameters for individual models are obtained by optimization
  2. Individual dynamics and community dynamics are simulated
  3. Figures for the manuscript are assembled from the results.

Type: Common Workflow Language

Creators: None

Submitter: David James Sherman

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