📄 Generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings

This repository contains the code used for the experiments in the paper:

Generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings by Diane Duroux, Paul P. Meyer, Giovanni Visonà, and Niko Beerenwinkel.

⚙️ Install the dependencies

You can set up the project with either pip or uv.

Option A - pip:

Install the ...

The bioinformatic workflow presented here enables the analysis of RNA sequencing data obtained from human reproductive tissues in unexplained recurrent pregnancy loss (uRPL) research. This pipeline requires a sample sheet containing the sample information (example_input_data.csv) and gene expression matrices generated using the Salmon tool in the nf-core/rnaseq bioinformatics pipeline (example_count_data.csv). For more information on how to use the nf-core/rnaseq pipeline including the required ...

Workflow for Metagenomics binning from assembly.

Minimal inputs are: Identifier, assembly (fasta) and an associated sorted BAM file

Summary

• MetaBAT2 (binning)
• MaxBin2 (binning)
• SemiBin2 (binning)
• Binette (bin merging)
• EukRep (eukaryotic classification)
• CheckM2 (bin completeness and contamination)
• BUSCO (bin completeness)
• GTDB-Tk (bin taxonomic classification)
• CoverM (bin abundances)

Including: Bin annotation (workflow: https://workflowhub.eu/workflows/1170):

• Bakta

...

MAGNETO is an automated snakemake workflow dedicated to MAG (Metagenome-Assembled Genomes) reconstruction from metagenomic data.

It includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery.

Key Features

• Quality Control (QC): Automatically assesses the quality and the contamination of input reads, ensuring that low-quality data are filtered out to improve downstream ...

This project is an analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes. It has been widely tested on human RNA sequencing from an Illumina HiSeq but should work on most systems and many other species, provided the necessary resource files can be downloaded.

Description

This pipeline is set for paired-end data only from Illumina HiSeq output files.

The main steps of the pipeline are:

• optionnal cleaning data with ...

Soil Metagenome Pipeline

Soil Metagenome Pipeline is a modular, Nextflow DSL2 workflow for assembling, polishing, binning, annotating, and functionally characterizing complex soil metagenomes. It orchestrates state-of-the-art tools for long- and short-read metagenomics, generates high-quality MAGs, assigns taxonomy, and screens for biosynthetic gene clusters (BGCs).

What it does

• Assembles long-read metagenomes (e.g., ONT) with Flye and optionally polishes with Medaka and/or NextPolish using ...

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2.
In addition files are exported to their respective subfolders for easier data management in a later stage.

Steps:

• Quality plots (FastQC)
• NG-TAX 2 High-throughput Amplicon Analysis
• PICRUSt 2 - Function prediction from marker gene sequences
• Export module for ngtax

Description

The Settlement Delineation and Analysis (SDA) workflows generates a settlement network from geospatial settlement data. It can process geotiff and shapefile inputs and was originally designed to operate on the World Settlement Footprint dataset. Through multiple workflow stages, a settlement network is constructed, contracted (i.e. clustered) and ultimately analysed with centrality measures. The output shapefile stores the ...

cfDNA-Flow

1. Overview

cfDNA-Flow facilitates the accurate and reproducible analysis of cfDNA WGS data. It offers various preprocessing options to accommodate different experimental setups and research needs in the field of liquid biopsies.

2. Preprocessing options

2.1 Trimming Options

cfDNA-Flow provides the flexibility to either trim or not trim the input reads based on the user's requirements. Trimming removes low-quality bases, which can impact downstream analyses.

2.2 Reference

...

🧬 Click-qPCR 🧬

An ultra-simple tool for interactive qPCR data analysis developed with R and Shiny.

日本語版のユーザーガイドはこちら (Read this document in Japanese)

Overview

Click-qPCR is a user-friendly Shiny web application designed for the straightforward analysis of real-time quantitative PCR (qPCR) data.

This tool is readily accessible via a web browser at , requiring no local installation for end-users.

It allows users to upload their Cq (quantification cycle) values, perform ΔCq ...