Workflows

What is a Workflow?
297 Workflows visible to you, out of a total of 320
Work-in-progress

The simplest workflow among a collection of workflows intended to solve tasks up to CTF estimation.

Type: Scipion

Creators: None

Submitter: Daniel Marchan

IMPaCT program

IMPaCT IMPaCT-isciii IMPaCT-Data ...

Type: Nextflow

Creators: Arnau Soler Costa, Amy Curwin, Jordi Rambla, All the Sarek team, nf-core comunity and people in the IMPaCT-Data project.

Submitter: Arnau Soler Costa

DOI: 10.48546/workflowhub.workflow.1030.2

Stable

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo ...

Type: Nextflow

Creators: Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Susan Thomson, Cecilia Deng

Submitter: Usman Rashid

Work-in-progress

Workflow for gene set enrichment analsysis (GSEA) and co-expression analysis (WGCNA) on transcriptomics data to analyze pathways affected in Porto-Sinusoidal Vascular Disease.

Type: Common Workflow Language

Creators: Aishwarya Iyer, Friederike Ehrhart

Submitter: Aishwarya Iyer

DOI: 10.48546/workflowhub.workflow.1040.1

Stable

Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)

Type: Galaxy

Creator: Peter van Heusden

Submitter: Peter van Heusden

Stable

Variant Interpretation Pipeline (VIP) that annotates, filters and reports prioritized causal variants in humans, see https://github.com/molgenis/vip for more information.

Type: Unrecognized workflow type

Creators: None

Submitter: Dennis Hendriksen

Stable

CNVand

Snakemake Conda Docker License [![Contributor ...

Type: Snakemake

Creator: Carlos Classen

Submitter: Carlos Classen

DOI: 10.48546/workflowhub.workflow.1039.1

Stable

pod5_by_pore

A Snakemake workflow to take the POD5 files produced by an Oxford Nanopore sequencing run and re-batch them by pore (ie. by channel).

This is useful if you want to run duplex basecalling because you can meaningfully run "dorado duplex" on a single (or a subset of) the POD5 files.

Know issues

It is assumed all POD5 input files are from the same sequencing run, but this is not checked.

Type: Snakemake

Creator: Tim Booth

Submitter: Tim Booth

beacon-omop-worker-workflows

Type: Common Workflow Language

Creators: None

Submitter: Vasiliki Panagi

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 ...

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