Workflows

What is a Workflow?
747 Workflows visible to you, out of a total of 808
End-to-end EI+ mass spectra prediction workflow using QCxMS
Stable

High-Performance Computing (HPC) environments are integral to quantum chemistry and computationally intense research, yet their complexity poses challenges for non-HPC experts. Navigating these environments proves challenging for researchers lacking extensive computational knowledge, hindering efficient use of domain specific research software. The prediction of mass spectra for in silico annotation is therefore inaccessible for many wet lab scientists. Our main goal is to facilitate non-experts ...

Type: Galaxy

Creators: Zargham Ahmad, Helge Hecht, Wudmir Rojas, RECETOX SpecDat

Submitters: Helge Hecht, Wudmir Rojas

DOI: 10.48546/workflowhub.workflow.897.2

Differential peak analysis with SnapATAC2

This workflow takes a cell-type-annotated AnnData object (processed with SnapATAC2) and performs peak calling with MACS3 on the cell types. Next, a cell-by-peak matrix is constructed and differential accessibility tests are performed for comparison of either two cell types or one cell type with a background of all other cells. Lastly, differentially accessible marker regions for each cell type are identified.

Type: Galaxy

Creator: Timon Schlegel

Submitter: Timon Schlegel

Multisample Batch Correction with SnapATAC2 and Harmony

This Workflow takes a dataset collection of single-cell ATAC-seq fragments and performs:

  • preprocessing
  • filtering
  • concatenation
  • dimension reduction
  • batch correction (with Harmony and optionally Scanorama and MNC-correct)
  • leiden clustering
  • new SnapATAC2 version: from 2.5.3 to 2.6.4

Type: Galaxy

Creators: None

Submitter: Timon Schlegel

Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2

Workflow for Single-cell ATAC-seq standard processing with SnapATAC2. This workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2. Finally, the clusters are manually annotated with the help of marker genes. In an alternative step, the fragment file can also be generated from a BAM file.

  • newer Version: Updated SnapATAC2 version from 2.5.3 to 2.6.4

Type: Galaxy

Creator: Timon Schlegel

Submitter: Timon Schlegel

Java COMPSs Matrix Multiplication, out-of-core using files, reproducible example, data persistence False, MareNostrum V
Stable

Name: Matrix Multiplication Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Matrix multiplication is a binary operation that takes a pair of matrices and produces another matrix.

If A is an n×m matrix and B is an m×p matrix, the result AB of their multiplication is an n×p matrix defined only if the number of columns m in A is equal to the number of rows m in B. When multiplying A and B, the elements of the ...

Type: COMPSs

Creator: Raül Sirvent

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.1088.1

Java COMPSs Matrix Multiplication, out-of-core using files, reproducible example, data persistence True
Stable

Name: Matrix Multiplication Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Matrix multiplication is a binary operation that takes a pair of matrices and produces another matrix.

If A is an n×m matrix and B is an m×p matrix, the result AB of their multiplication is an n×p matrix defined only if the number of columns m in A is equal to the number of rows m in B. When multiplying A and B, the elements of the ...

Type: COMPSs

Creator: Raül Sirvent

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.1086.1

BY-COVID WP5 T5.2 Baseline Use Case
Work-in-progress

This publication corresponds to the Research Objects (RO) of the Baseline Use Case proposed in T.5.2 (WP5) in the BY-COVID project on “COVID-19 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection”.

Type: Quarto Markdown

Creators: Enrique Bernal-Delgado, Nina Van Goethem, Francisco Estupiñan-Romero, Marjan Meurisse, Javier González Galindo, Natalia Martínez-Lizaga, Santiago Royo-Sierra

Submitter: Marjan Meurisse

DOI: 10.48546/workflowhub.workflow.502.4

cocomico_wf_simulated

CoCoMiCo analyses on collections of simulated communities. Community: scatterplots and KW tests of cooperation and competition potentials, for each collection. Similarity: cooperation and competition potentials vs model similarity, defined as the Jaccard distance on sets of reactions. Added value: boxplots comparing the added value of models in communities.

Type: Common Workflow Language

Creators: None

Submitter: David James Sherman

Lysozyme in water full, no MPI
Stable

Lysozyme in water full COMPSs application

Type: COMPSs

Creator: Javier Conejero

Submitter: Raül Sirvent

Lysozyme in water, using dataset_small, data_persistence True
Stable

Lysozyme in water full COMPSs application, using dataset_small

Type: COMPSs

Creator: Rosa M. Badia

Submitter: Raül Sirvent

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