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738 Workflows visible to you, out of a total of 793
CWL-based RNA-Seq workflow
Stable

A CWL-based pipeline for processing RNA-Seq data (FASTQ format) and performing differential gene/transcript expression analysis.

On the respective GitHub folder are available:

  • The CWL wrappers for the workflow
  • A pre-configured YAML template, based on validation analysis of publicly available HTS data
  • A table of metadata (mrna_cll_subsets_phenotypes.csv), based on the same validation analysis, to serve as an input example for the design of comparisons during differential expression ...

Type: Common Workflow Language

Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos

Submitter: Konstantinos Kyritsis

DOI: 10.48546/workflowhub.workflow.524.1

SARS-CoV-2 Illumina Amplicon pipeline - SANBI - v1.2

SARS-CoV-2 variant prediction using Read It And Keep, fastp, bbmap and iVar

Type: Galaxy

Creators: Peter van Heusden, Bradley W. Langhorst

Submitter: Peter van Heusden

SARS-CoV-2 ONT Amplicon Sequencing SANBI 1.0
No description specified

Type: Galaxy

Creators: None

Submitter: Peter van Heusden

SARS-CoV-2 PostProcessing
No description specified

Type: Galaxy

Creators: None

Submitter: Peter van Heusden

Life Science cross-RI (Research Infrastructure) project
Stable

The project allowed us to manage and build structured code scripts on the Jupyter Notebook, a simple web application which is user-friendly, flexible to use in the research community. The script is developed to address the specific needs of research between different platforms of dataset. These stakeholders have developed their own platforms for the annotation and standardisation of both data and metadata produced within their respective field. -The INFRAFRONTIER - European Mutant Mouse Archive ...

Type: Jupyter

Creator: Elisabetta Spinazzola

Submitter: Elisabetta Spinazzola

Metagenome and metatranscriptome assembly in CWL
Stable

CWL-assembly

Codacy Badge Build Status

Description

This repository contains two workflows for metagenome and ...

Type: Common Workflow Language

Creators: None

Submitters: Germana Baldi, Varsha Kale

CroMaSt: A workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment
Stable

CroMaSt: A workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment

CroMaSt (Cross Mapper of domain Structural instances) is an automated iterative workflow to clarify the assignment of protein domains to a given domain type of interest, based on their 3D structure and by cross-mapping of domain structural instances between domain databases. CroMaSt (for Cross-Mapper of domain Structural instances) ...

Type: Common Workflow Language

Creators: Hrishikesh Dhondge, Isaure Chauvot de BeauchĂȘne, Marie-Dominique Devignes

Submitter: Hrishikesh Dhondge

DOI: 10.48546/workflowhub.workflow.390.2

Nucleoli segmentation using CellProfiler (EOSC-Life D6)
Stable

This workflow has been created as part of Demonstrator 6 of the project EOSC-Life (within WP3) and is focused on reusing publicly available RNAi screens to gain insights into the nucleolus biology. The workflow downloads images from the Image Data Resource (IDR), performs object segmentation (of nuclei and nucleoli) and feature extraction of the images and objects identified.

Tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/tutorial.html

Type: Galaxy

Creators: None

Submitter: Beatriz Serrano-Solano

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Gene similariy anaylsis across physiological systems in IMPC phenotype data

Gene similariy anaylsis across physiological systems in IMPC phenotype data

A Jupyter Notebook tool for analysing user specified genes across the different physiological systems in IMPC data.

Input

The tool takes as input a list of gene ids (MGI ids or Gene Symbol ids). The elemnts in the list could be separated by a comma, semicolumn, tab or newline.

Operation

The program will create an heatmap representing the number of phenotypes and the mp term list for each gene contained in ...

Type: Jupyter

Creators: Andrea Furlani, Philipp Gormanns

Submitter: Andrea Furlani

Performance evaluation of Katdetectr and other kataegis detection packages
Stable

Introduction

This repository contains all the custom scripts used in the evaluation and comparison of Katdetectr as described in the corresponding Technical Note (under submission).

Usage

All required files were deposited on Zenodo. These can directly be downloaded using zen4R and be used as input.

# Increase the timeout (due to some large files). 
options(timeout=5000)
...

Type: R markdown

Creators: Daan Hazelaar, Job van Riet

Submitter: Daan Hazelaar

DOI: 10.48546/workflowhub.workflow.500.1

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