Workflows

What is a Workflow?
1255 Workflows visible to you, out of a total of 1336
Stable

Colorectal-cancer-detection-using-ColoPola-dataset

Methods

We trained and tested three models from scratch (CNN, CNN_2 and EfficientFormerV2) and two pretrained models (DenseNet121 and EfficientNetV2-m) to classify the colorectal cancer using the ColoPola dataset.

ColoPola dataset

The dataset consists of 572 slices (specimens) with 20,592 images. There are 284 cancer samples and 288 normal samples. This dataset can download from Zenodo repository. ...

Type: Python

Creators: Thi-Thu-Hien Pham, Thao-Vi Nguyen, The-Hiep Nguyen, Quoc-Hung Phan, Thanh-Hai Le

Submitter: Thanh-Hai Le

DOI: 10.48546/workflowhub.workflow.1797.1

CryoDataBot

CryoDataBot is an automated pipeline designed to streamline dataset generation for cryogenic electron microscopy (cryoEM)-based atomic model building. It supports large-scale AI training and benchmarking by providing standardized tools for data retrieval, preprocessing, labeling, and quality control. CryoDataBot enables flexible configurations for diverse biomolecular structures, improves modeling reproducibility, and facilitates retraining of AI models such as U-Net and CryoREAD. ...

Type: Python

Creators: Qibo Xu, Hong Zhou, Leon Wu, Micahel Rebelo, Shi Feng, Star Yu, Farhanaz Farheen, Daisuke Kihara

Submitter: Qibo Xu

DOI: 10.48546/workflowhub.workflow.1796.1

Work-in-progress

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite with ...

Type: Nextflow

Creators: Huihai Wu, Irene Papatheodorou, Yuxuan Lan, David Swarbreck

Submitter: Huihai Wu

qcif/taxodactyl is a modular, reproducible Nextflow workflow for the conservative taxonomy assignment to DNA sequences, designed for high-confidence, auditable results in biosecurity and biodiversity contexts. The workflow integrates multiple bioinformatics tools and databases, automates best-practice analysis steps, and produces detailed reports with supporting evidence for each taxonomic assignment.

Workflow Overview

The pipeline orchestrates a series of analytical steps, each encapsulated ...

Type: Nextflow

Creators: Magdalena Antczak, Cameron Hyde, Lanxi (Daisy) Li, Valentine Murigneux, Sarah Williams, Michael Thang, Bradley Pease, Shaun Bochow, Grace Sun

Submitter: Magdalena Antczak

DOI: 10.48546/workflowhub.workflow.1782.3

Prediction of HLA binding for verified candidates

Associated Tutorial

This workflows is part of the tutorial Neoantigen 5a: Predicting HLA Binding, available in the GTN

Features

Thanks to...

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Type: Galaxy

Creators: None

Submitter: GTN Bot

Merging Fusion and non-normal databases + Discovery peptidomics using FragPipe

Associated Tutorial

This workflows is part of the tutorial Neoantigen 2: Database merge and FragPipe discovery, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: GTN Bot

Create a protein Fusion database through the Arriba workflow

Associated Tutorial

This workflows is part of the tutorial Neoantigen 1a: Fusion-Database-Generation, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: GTN Bot

Validate the NeoAntigen Candidates from FragPipe discovery through the PepQuery Novel search

Associated Tutorial

This workflows is part of the tutorial Neoantigen 3: PepQuery2 Verification, available in the GTN

Features

Type: Galaxy

Creators: None

Submitter: GTN Bot

Annotating the novel peptides

Associated Tutorial

This workflows is part of the tutorial Neoantigen 4: Variant Annotation, available in the GTN

Features

Thanks to...

Workflow Author(s): GalaxyP ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

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