Workflows
What is a Workflow?Filters
Image processing from movies to micrographs, including CTF estimation and quality filters for image curation.
Adapting to Tilted Samples
To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:
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Motion Correction Filters: Max per-frame shift = 30; Global drift = 120.
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CTF Consensus Filters: Adapted to 6.5 Å and 8.5 Å resolution cutoffs.
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**Defocus ...
Image processing pipeline from movies to micrographs, including CTF estimation and quality filters for image curation.
The idea of this workflow is to compare annotation with two annotation tools that differ in their approach and operation.
Associated Tutorial
This workflows is part of the tutorial Comparison of two annotation tools - Helixer and Braker3, available in the GTN
Features
- Includes [Galaxy Workflow ...
Metatranscriptomics analysis using microbiome RNA-seq data
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Associated Tutorial
This workflows is part of the tutorial Metatranscriptomics analysis using microbiome RNA-seq data (short), available in the GTN
Features
- Includes Galaxy Workflow Tests ...
Perform background subtraction, nuclear segmentation, feature quantification, cellular phenotyping, spatial analysis, and interactive visualization of registered TMA core multiplex tissue images
ONTeater is a eukaryotic genome assembly pipeline intended to produce highly-contiguous genomes with a single input of Oxford NanoPore Tech (ONT) longread data, although PacBio is accepted as well. Information can be found here. Originally developed to support genome assembly efforts by OIKOS genomics, predominantly of nonmodel vertebrate species.
A Retrieval-Augmented Knowledge Mining Method with Deep Thinking LLMs for Biomedical Research and Clinical Support
Introduction
Knowledge graphs and large language models (LLMs) serve as key tools for biomedical knowledge integration and reasoning, facilitating the structured organization of literature and the discovery of deep semantic relationships. However, existing methods still face challenges in knowledge mining and cross-document reasoning: knowledge graph construction is constrained ...