Workflows
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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 ...
Type: Python
Creators: Bundit Boonyarit, Matin Kositchutima, Tisorn Na Phattalung, Nattawin Yamprasert, Chanitra Thuwajit, Thanyada Rungrotmongkol, Sarana Nutanong
Submitter: Bundit Boonyarit
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 ...
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Laura Leroi, Patrick Durand, Laure Quintric
Submitter: Cyril Noel
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 ...
Type: Nextflow
Creators: Veit Schwämmle, Magnus Palmblad
Submitters: Laura Rodriguez-Navas, José Mª Fernández
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. ...
Associated Tutorial
This workflows is part of the tutorial Deep Learning (Part 2) - Recurrent neural networks (RNN), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Kaivan Kamali
Tutorial Author(s): [Kaivan ...
Final output is a table of Taxa and how many sequences aligned with them. This table can be used to then visualize via a pie chart.
Associated Tutorial
This workflows is part of the tutorial Taxonomic Analysis of eDNA, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Age prediction using machine learning
Associated Tutorial
This workflows is part of the tutorial Age prediction using machine learning, available in the GTN
Thanks to...
Tutorial Author(s): Ekaterina Polkh, [Anup ...
Age prediction using machine learning
Associated Tutorial
This workflows is part of the tutorial Age prediction using machine learning, available in the GTN
Thanks to...
Tutorial Author(s): Ekaterina Polkh, [Anup ...
Basics of machine learning
Associated Tutorial
This workflows is part of the tutorial Basics of machine learning, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): [Anup ...
Interval-Wise Testing for omics data
Associated Tutorial
This workflows is part of the tutorial Interval-Wise Testing for omics data, available in the GTN
Thanks to...
Tutorial Author(s): Marzia A Cremona, Fabio Cumbo ...