Workflows
What is a Workflow?Filters
CausalCoxMGM
Implementation of CausalCoxMGM algorithm and scripts for analysis of simulated and real-world biomedical datasets.
Installation
To install CoxMGM and CausalCoxMGM, run the following command in the terminal:
R CMD INSTALL rCausalMGM
or alternatively:
R CMD INSTALL rCausalMGM/rCausalMGM_1.0.tar.gz
Demonstration of CausalCoxMGM with the WHAS500 dataset
First, we begin by loading the necessray R packages for this analysis.
library(rCausalMGM)
library(survival)
...
This workflow was developed for the 2024 Bioinformatics Bootcamp at The Open University. It imports datasets from the EBI SCXA, reformats then, and analyses them similar to the Filter, plot and explore Galaxy tutorial.
Type: Galaxy
Creators: Wendi Bacon, Julia Jakiela, The Open University
Submitter: Diana Chiang Jurado
The Galaxy workflow for clonal population analysis was designed to process patient mutation data extracted from cBioPortal, specifically using the TracerX study as an example. This workflow, part of the deliverable D3.2 for EOSC4Cancer developed at UiO, begins with a raw patient mutation table from cBioPortal, where modifications and formatting occur to prepare the data for analysis. Some data, notably the copy number alterations (referred to as "All_CN"), were manually uploaded to Galaxy to ...
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 ...
Type: Nextflow
Creators: Gisela Gabernet, Simon Heumos, Alexander Peltzer
Submitter: WorkflowHub Bot
This workflow constructs Metagenome-Assembled Genomes (MAGs) using SPAdes or MEGAHIT as assemblers, followed by binning with four different tools and refinement using Binette. The resulting MAGs are dereplicated across the entire input sample set, then annotated and evaluated for quality. You can provide pooled reads (for co-assembly/binning), individual read sets, or a combination of both. The input samples must consist of the original reads, which are used for abundance estimation. In all cases, ...
Type: Galaxy
Creators: Bérénice Batut, Paul Zierep, Mina Hojat Ansari, Patrick Bühler, Santino Faack
Submitter: WorkflowHub Bot
This workflow can be used to assign multi-element molecular formulas to ultrahigh resolution mass spectra.
Workflow to predict EI mass spectra using QCxMS starting from a single SDF file, containing the 3D coordinates of all atoms in the molecule. These files can typically be obtained from PubChem.