Workflow for Creating a large disease network from various datasets and databases for IBM, and applying the active subnetwork identification method MOGAMUN.

Cancer Invasion Workflow

Table of Contents

• Cancer Invasion Workflow
• Table of Contents
• Description
• Contents
• Building Blocks
• Workflows
• Resources
• Tests
• Instructions
• Local machine
• Requirements
• Usage steps
• MareNostrum 4
• [Requirements in ...

Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment

Introduction

Phylogeny refers to the evolutionary history and relationship between biological lineages related by common descent. Reticulate evolution refers to the origination of lineages through the complete or partial merging of ancestor lineages. Networks may be used to represent lineage independence events in non-treelike phylogenetic processes.

The methodology for reconstructing networks ...

Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data

Hall, M, Coin, L., Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data. bioRxiv 2023. doi: [10.1101/2023.09.18.558339][doi]

Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and classification of M. tuberculosis reads.

This repository contains the code and ...

BACPAGE

This repository contains an easy-to-use pipeline for the assembly and analysis of bacterial genomes using ONT long-read or Illumina short-read technology. Read the complete documentation and instructions for bacpage and each of its functions here

Introduction

Advances in sequencing technology during the COVID-19 pandemic has led to massive increases in the generation of sequencing data. Many bioinformatics tools ...

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This repository contains an easy-to-use pipeline for the assembly and analysis of bacterial genomes using ONT long-read or Illumina short-read technology.

Introduction

Advances in sequencing technology during the COVID-19 pandemic has led to massive increases in the generation of sequencing data. Many bioinformatics tools have been developed to analyze this data, but very few tools ...

Snakemake workflow: dna-seq-varlociraptor

A ...

ANNOTATO - Annotation workflow To Annotate Them Oll

• ANNOTATO - Annotation workflow To Annotate Them Oll
• Overview of the workflow
• Input data
• Pipeline steps
• Output data
• Prerequisites
• Installation
• Running ANNOTATO
• Before running the pipeline (IMPORTANT) ...

Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data

In recent years, convolutional neural network (CNN)-based methods have shown remarkable performance in the denoising and reconstruction of super-resolved structured illumination microscopy (SR-SIM) data. Therefore, CNN-based architectures have been the main focus of existing studies. Recently, however, an alternative and highly competitive deep learning architecture, ...

A pipeline for mapping, calling, and annotation of SARS-CoV2 variants.