Workflows
What is a Workflow?Filters
The Spatial Transcriptomics analysis workflow for Xenium data from the PATH2XNAT project tested on the non-diseased lung dataset from 10X genomics. The analysis workflow written in R and executed in the interactive RStudio environment consists of visualizations, clustering, feature selection and cluster annotation.
RNA-SeqEZPZ-NF
Nextflow Pipeline for RNA-SeqEZPZ
A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations
RNA-SeqEZPZ-NF is another implementation of RNA-SeqEZPZ. RNA-SeqEZPZ-NF uses the same user interface as RNA-SeqEZPZ and runs the same pipeline, but runs the pipeline implemented by Nextflow. This pipeline is currently tested on HPC cluster with SLURM scheduler. Advanced ...
RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations
RNA-SeqEZPZ is a pipeline to run analysis of RNA-Seq experiments from raw FASTQ files all the way to differential genes analysis. The pipeline is accessible through a graphical user interface implemented using a Shiny app and features interactive plots. Advanced users have the ability to customize the scripts provided with the pipeline. This pipeline is designed to run on an HPC ...
SciWIn Client Demo
A basic Workflow using SciWIn Client (s4n
) can be created with the commands hereafter. This guide assumes the usage of unix based operating systems, however Windows should work, too. If not please open an issue.
Installation
📄 Generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings
This repository contains the code used for the experiments in the paper:
Generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings by Diane Duroux, Paul P. Meyer, Giovanni Visonà, and Niko Beerenwinkel.
⚙️ Install the dependencies
Clone the repository, unzip OriginalData.zip, and install the necessary dependencies ...
MAGNETO
MAGNETO is an automated snakemake workflow dedicated to MAG (Metagenome-Assembled Genomes) reconstruction from metagenomic data.
It includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery.
Key Features
- Quality Control (QC): Automatically assesses the quality and the contamination of input reads, ensuring that low-quality data are filtered out to improve ...
Type: Snakemake
Creators: Samuel Chaffron, Audrey Bihouee, Benjamin Churcheward, Maxime Millet, Guillaume Fertin, Hugo Lefeuvre
Submitter: Hugo Lefeuvre
Based on the Tail analysis workflow at https://git.embl.org/grp-cba/tail-analysis/-/blob/main/analysis_workflow.md
DUNE: Deep feature extraction by UNet-based Neuroimaging-oriented autoEncoder
A versatile neuroimaging encoder that captures brain complexity across multiple diseases: cancer, dementia and schizophrenia.
Overview
DUNE (Deep feature extraction by UNet-based Neuroimaging-oriented autoEncoder) is a neuroimaging-oriented deep learning model designed to extract deep features from multisequence brain MRIs, enabling their processing by basic machine learning algorithms. This project provides an ...