SynProtX

An official implementation of our research paper "SynProtX: A Large-Scale Proteomics-Based Deep Learning Model for Predicting Synergistic Anticancer Drug Combinations".

SynProtX is a deep learning model that integrates large-scale proteomics data, molecular graphs, and chemical fingerprints to predict synergistic effects of anticancer drug combinations. It provides robust ...

SAMBA is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to conduct reproducible eDNA analyses using Nextflow. SAMBA starts processing by verifying integrity of raw reads and metadata. Then all bioinformatics processing is done using commonly used procedure (QIIME 2 and DADA2) but adds new steps relying on dbOTU3 and microDecon to build high quality ASV count tables. Extended statistical analyses are also performed. Finally, SAMBA ...

Introduction

wombat-p pipelines is a bioinformatics analysis pipeline that bundles different workflow for the analysis of label-free proteomics data with the purpose of comparison and benchmarking. It allows using files from the proteomics metadata standard SDRF.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses ...

Click-qPCR

Ultra-simple tool for interactive qPCR data analysis developed by R and Shiny.

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

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 https://kubo-azu.shinyapps.io/Click-qPCR/, requiring no local installation for end-users. ...

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)

A workflow for performing alignment and phylogeny using protein sequences from the CrusTome database. See crustybase.org/crustome for more information.

Calculate extended gamma-ray source halo using crbeam simulation