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CausalCoxMGM

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)
...

Type: R markdown

Creators: None

Submitter: Tyler Lovelace

Import and Analyse from EBI - Universal
Stable

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

nf-core/nascent

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

Type: Nextflow

Creators: Ignacio Tripodi, Margaret Gruca

Submitter: WorkflowHub Bot

Clonal population analysis for TracerX study

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 ...

Type: Galaxy

Creators: None

Submitter: Jeanne Chèneby

DOI: 10.48546/workflowhub.workflow.1355.1

Photometric Redshift Estimation for Candidate Optical Counterparts of Astronomical Sources Extracted from Texts
Work-in-progress
No description specified

Type: Galaxy

Creators: None

Submitter: Andrei Variu

PVGA

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: Python

Creator: Zhi Song

Submitter: Zhi Song

DOI: 10.48546/workflowhub.workflow.1305.1

nf-core/airrflow

GitHub Actions CI Status GitHub Actions Linting Status AWS CI ...

Type: Nextflow

Creators: Gisela Gabernet, Simon Heumos, Alexander Peltzer

Submitter: WorkflowHub Bot

mags-building/main

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

mfassignr/main

This workflow can be used to assign multi-element molecular formulas to ultrahigh resolution mass spectra.

Type: Galaxy

Creators: Kristina Gomoryova, Helge Hecht, RECETOX, MUNI

Submitter: WorkflowHub Bot

qcxms-sdf/main

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.

Type: Galaxy

Creators: Helge Hecht, RECETOX

Submitter: WorkflowHub Bot

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