Workflows

What is a Workflow?
831 Workflows visible to you, out of a total of 904
OMERO Image Import, Annotation and Region of Interests (ROIs) Workflow
Stable

General workflow to upload data into OMERO using Galaxy

A dataset for testing can be found at: https://zenodo.org/records/14205500

Important Security Note: It is crucial to be aware that storing credentials as variables can pose security risks, particularly if accessed by administrators. Therefore, it is essential to handle user credentials securely and in accordance with best practices.

Type: Galaxy

Creators: Riccardo Massei, Matthias Bernt, Riccardo Massei

Submitter: Riccardo Massei

DOI: 10.48546/workflowhub.workflow.1258.1

OMERO Image Import and Annotation Workflow
Stable

General workflow to upload data into OMERO using KNIME

The workflow consists of two main branches: the Green Branch, which imports a folder containing images, and the Purple Branch, which enables the annotation of metadata as key-value pairs.

  • Fetching Images: The first step involves fetching images from a locally accessible folder.
  • User Authentication: Users are prompted to input their OMERO username and password through a Java snippet. This information is then converted into ...

Type: KNIME

Creator: Riccardo Massei

Submitter: Riccardo Massei

nf-core/nanostring

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: Peltzer , Alexander & Mohr, Christopher

Submitter: WorkflowHub Bot

scanpy-clustering/main

Single-cell RNA-seq workflow with Scanpy and Anndata. Based on the 3k PBMC clustering tutorial from Scanpy. It takes count matrix, barcodes and feature files as input and creates an Anndata object out of them. It then performs QC and filters for lowly expressed genes and cells. Then the data is normalized and scaled. Then PCs are computed to further cluster using louvain algorithm. It also generated various plots of clustering colored with highly ranked genes.

Type: Galaxy

Creators: Pavankumar Videm, Hans-Rudolf Hotz, Mehmet Tekman, Bérénice Batut

Submitter: WorkflowHub Bot

annotation-helixer/main

This workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.

Type: Galaxy

Creator: Romane Libouban

Submitter: WorkflowHub Bot

Allele-specific expression-network clustering analysis for Huntington's Disease
No description specified

Type: Common Workflow Language

Creators: None

Submitter: Aishwarya Iyer

nf-core/pixelator

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creator: Pixelgen Technologies AB

Submitter: WorkflowHub Bot

mettannotator
Stable

Nextflow run with docker run with singularity

mettannotator

Type: Nextflow

Creators: Tatiana Gurbich, Martin Beracochea

Submitter: Martin Beracochea

A workflow to extract individual trees from 3D point cloud data obtained by airborne laser scanning

Point-based Individual Tree Delineation from 3D LiDAR Point Cloud Data.

This module implements a lightweight and easy-to-use Point-based method for individual tree delineation from 3D point cloud data using pure C/C++.

The source code files are included in folder [TreeSeparation], which consists of a project generated from Visual Studio 2015. The CLASS for tree separation is named "FoxTree" and can be found in the respect FoxTree.h and FoxTree.cpp files.

Inupt

The ...

Type: Unrecognized workflow type

Creators: None

Submitter: Jinhu Wang

nf-core/rangeland

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: None

Submitter: WorkflowHub Bot

Powered by
 (v.1.16.0)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH