Based on the Tail analysis workflow at https://git.embl.org/grp-cba/tail-analysis/-/blob/main/analysis_workflow.md

DUNE: Deep feature extraction by UNet-based Neuroimaging-oriented autoEncoder

A versatile neuroimaging encoder that captures brain complexity across multiple diseases: cancer, dementia and schizophrenia.

Overview

DUNE (Deep feature extraction by UNet-based Neuroimaging-oriented autoEncoder) is a neuroimaging-oriented deep learning model designed to extract deep features from multisequence brain MRIs, enabling their processing by basic machine learning algorithms. This project provides an ...

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. ...

This workflow extracts protein-coding sequences from whole genome sequencing (WGS) data obtained from the European Nucleotide Archive (ENA). It automates the preprocessing, annotation, and selection of relevant protein sequences using tools such as Prokka, FASTA-to-Tabular, and pattern-based selection. The resulting dataset supports downstream analyses including comparative genomics, phylogenetics, and functional annotation.

GenErode pipeline

GitHub repository for GenErode, a Snakemake workflow for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.

Documentation

The full pipeline documentation can be found on the repository wiki.

Citation

If you've ...

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle ...

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using Relion.

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:

• Motion Correction Filters: Max ...