Workflow to download and prepare TCGA data.

The workflow divides the process of generating Gene Regulatory networks from TCGA cancer data in three steps:

1. Downloading the raw data from GDC and saving the rds/tables needed later
2. Preparing the data. This step includes filtering the data, normalizing it...
3. Analysis of gene regulatory networks

PVGA is a powerful virus-focused assembler that does both assembly and polishing. For virus genomes, small changes will lead to significant differences in terms of viral function and pathogenicity. Thus, for virus-focused assemblers, high-accuracy results are crucial. Our approach heavily depends on the input reads as evidence to produce the reported genome. It first adopts a reference genome to start with. We then align all the reads against the reference genome to get an alignment graph. After ...

This workflow demonstrates the integration of FAIR principles into the workflow management ecosystem through provenance integration in Autosubmit, a workflow manager developed at the Barcelona Supercomputing Center (BSC), and SUNSET (SUbseasoNal to decadal climate forecast post-processing and aSSEssmenT suite), an R-based verification workflow also developed at BSC.

Autosubmit supports the generation of data provenance information based on RO-Crate, facilitating the creation of machine-actionable ...

Calculate extended gamma-ray source halo using crbeam simulation

Crop Wild Relatives distribution modeling workflow using the ModGP; a prototype Digital Twin from BioDT.

Workflow to perform nuclei cell counting on High Content Screening (HCS) Data and upload result into OMERO

In this workflow, cell images are first uploaded to both Galaxy and OMERO using the “OMERO Image Import” tool. Concurrently, image processing is performed. After thresholding and binarization, key features of nuclei, such as area, label number, and perimeter, are computed from the processed images and saved as a CSV file. The result file is then attached to each image stored in OMERO using ...

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.

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 ...

The workflow starts with selecting EH38E2924876 as the search term. Genomic position of provided unique regulatory element identifier was retrieved from CFDE Linked Data Hub[1]. A list of variants in the region of the regulatory element was retrieved from CFDE Linked Data Hub[1]. Variant/variant set associated allele specific epigenomic signatures were retrieved from CFDE LDH[5] based on Roadmap and ENTEx data[6], [4]. GTEx eQTL and sQTL evidence for the given variant(s) were retrieved from CFDE ...