Bioimaging Data Management Workflow for Plasma Medicine

This repository contains the Jupyter notebook implementation of a bioimaging data management workflow for plasma medicine (see preprint and poster). The workflow is implemented as a structured pipeline integrating open-source tools, including OMERO for image data management, eLabFTW ...

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EXCON (v2.3.2)

A Nextflow pipeline for gene family EXpansion and CONtraction analysis across multiple species using CAFE5.

Given a set of genome assemblies and annotations, EXCON builds orthogroups with OrthoFinder, fits and compares multiple CAFE models to identify gene families evolving at significantly different rates, and automatically selects the best-fitting model for downstream analysis. Optionally, GO enrichment analysis can be run on expanded and contracted gene families, and ...

Phorager

Prophage Analysis Pipeline

A comprehensive pipeline for bacterial genome quality control, prophage detection, and prophage characterization

Authors:

• Xena Dyball
• James Docherty
• Alise Ponsero
• Ryan Cook

Citation: [Paper Citation or Preprint Link]

Overview

Phorager provides an integrated workflow for:

• Bacterial genome quality control - CheckM2 assessment, filtering, and dRep dereplication
• Prophage detection - GenoMAD and ...

CLIP-seq Workflow

A Nextflow workflow for end-to-end processing of CLIP-seq data, supporting multiple CLIP protocols.

Overview

Starting from raw FASTQ files (or un-demultiplexed iCLIP data), the workflow processes reads through quality control, adapter trimming, rRNA removal, genome alignment, and UMI deduplication, then runs shoji to extract crosslink sites and produce per-sample and combined count matrices ready for differential binding analysis (see ...

Petrisnake: A secondary analysis pipeline for PETRI-seq data.

This is a Snakemake pipeline for the secondary computational analysis of single cell RNA-seq data from the PETRI-seq protocol (https://www.nature.com/articles/s41564-020-0729-6 and https://www.nature.com/articles/s41586-024-08124-2), this is: From the input FASTQ files, this workflow constructs a gene count table showing the expression of each gene in each cell. Petrisnake is available on WorkflowHub (https://workflowhub.eu/workflows/2081). ...

Automated screening monitoring workflow designed to provide real-time feedback to the microscope during data acquisition. The pipeline processes movies on-the-fly, performing motion correction, maxshift analysis, CTF estimation and consensus validation, as well as micrograph quality assessment through AI-based categorization. The workflow also includes particle picking, automatic box size estimation, particle extraction, streaming 2D classification, and 2D class quality assessment. Results are ...

This workflow performs a basic Virtual Drug Screening Pipeline. THe workflows uses the following protocols: 1.a) Import receptor: Imports the atomic structure with PDB code 4ERF. 1.b) Import small molecules: Imports a set of 4 molecules from local files. 2.a) Receptor preparation: selects A chain and cleans the structure from waters and heteroatoms 2.b) RDKit Molecules preparation: adds hydrogens and prepares the molecules for docking 3.a) Find pockets: uses P2Rank to predict the most promising ...

IsoAnnot

IsoAnnot is a new tool for generating functional and structural annotation at isoform level, capable of collecting and integrating information from different databases to categorize and describe each isoform, including functional and structural information for both transcript and protein.

⚠️⚠️ IsoAnnot is currenlty under beta-testing. Please see the latest release and download IsoAnnot from the ...