Workflows
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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
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
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
Type: Nextflow
Creators: Alem Gusinac, Thomas Ederveen, Jos Boekhorst, Annemari Boleij
Submitter: Alem Gusinac
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
- Includes a Galaxy Workflow Report
Thanks to...
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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
- Includes a Galaxy Workflow Report ...
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
- Includes a Galaxy Workflow Report ...
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
- Includes a Galaxy Workflow Report ...
Annotating the novel peptides
Associated Tutorial
This workflows is part of the tutorial Neoantigen 4: Variant Annotation, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): GalaxyP ...