SeuratExtend: An Enhanced Toolkit for scRNA-seq Analysis

Overview

SeuratExtend is an R package designed to provide an improved and easy-to-use toolkit for scRNA-seq analysis and visualization, built upon the Seurat object. While Seurat is a widely-used tool in the R community that offers a foundational framework for scRNA-seq analysis, it has limitations when it comes to more advanced analysis and customized visualization. SeuratExtend expands upon Seurat by offering an array of ...

Annual percentage Change for population in Germany (1950 - 2025)

This workflow run was executed on Galaxy (Workflow Rerun Information)

Workflow: Climate Stripes

Execution Status: scheduled

Executed: 2025-05-27 14:14:07.240149

Workflow Inputs

Formal Input Definitions

• Germany-Population-Annual--Change-2025-05-27-15-17.csv (File)

• Column name to use for plotting (Text)

• Plot Title (Text)

• nxsplit (Integer)

• Description: Number of values per intervals

...

This is the workflow for thesis: A FAIR Data Pipeline for Ecosystem Research, with Machine Learning and Marine Acoustic Data (Jiamian He)

Calculate extended gamma-ray source halo using crbeam simulation

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 ...