This workflows contains a pipeline in Scipion that performs the following steps:

1.1) Import small molecules: introduces a set of small molecular structures in the pipeline as prospective ligands

1.2) Import atomic structure: introduces a protein atomic structure in the pipeline as receptor.

2.1) Ligand preparation: uses RDKit to prepare the small molecules optimizing their 3D structure.

2.2) Receptor preparation: uses bioPython to prepare the receptor structure, removing waters, adding hydrogens ...

This workflow performs the most basic Virtual Drug Screening Pipeline to import a set of small molecules and dock them to an imported protein structure.

BVSim: A Benchmarking Variation Simulator Mimicking Human Variation Spectrum

Table of Contents

• Getting Started
• Installation
• General Functions and Parameters
• Shared Parameters
• Output Naming Conventions
• [Write the Relative ...

CausalCoxMGM

Implementation of CausalCoxMGM algorithm and scripts for analysis of simulated and real-world biomedical datasets.

Installation

To install CoxMGM and CausalCoxMGM, run the following command in the terminal:

R CMD INSTALL rCausalMGM 

or alternatively:

R CMD INSTALL rCausalMGM/rCausalMGM_1.0.tar.gz 

Demonstration of CausalCoxMGM with the WHAS500 dataset

First, we begin by loading the necessray R packages for this analysis.

library(rCausalMGM) 
library(survival)
...

PVGA is a powerful virus-focused assembler that does both assembly and polishing. For virus genomes, small changes will lead to significant differences in terms of viral function and pathogenicity. Thus, for virus-focused assemblers, high-accuracy results are crucial. Our approach heavily depends on the input reads as evidence to produce the reported genome. It first adopts a reference genome to start with. We then align all the reads against the reference genome to get an alignment graph. After ...

Current version of this workflow: https://workflowhub.eu/workflows/1109. Please use only with the new version. KNIME workflow to gather ChEMBL permeability data is availbale: https://workflowhub.eu/workflows/1169.

gSpreadComp: Streamlining Microbial Community Analysis for Resistance, Virulence, and Plasmid-Mediated Spread

Overview

gSpreadComp is a UNIX-based, modular bioinformatics toolkit designed to streamline comparative genomics for analyzing microbial communities. It integrates genome annotation, gene spread calculation, plasmid-mediated horizontal gene transfer (HGT) detection and resistance-virulence ranking within the analysed microbial community to help researchers identify potential ...

AnnoAudit - Annotation Auditor

AnnoAudit is a robust Nextflow pipeline designed to evaluate the quality of genomic annotations through a multifaceted approach.

Overview of the workflow

The workflow assess the annotation quality based on different criteria:

• Protein evidence support
• RNASeq evidence support
• Statistics of the predictions (i.e., gene length, exon number, etc.)
• Ortholog analysis (BUSCO, OMArk)

Input data

• Reference genome genome.[.fna, .fa, .fasta]
• Annotation ...

Prostate cancer classification workflow

This workflow segments tissue regions and classifies prostate cancer on H&E whole slide images, using AI. It consists of three steps:

1. low-resolution tissue segmentation to select areas for further processing;

2. high-resolution tissue segmentation to refine borders - it uses step 1 as input;

3. high-resolution normal/cancer classification - it uses step 1 as input.