Workflows

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817 Workflows visible to you, out of a total of 891
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: [email protected] 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: [email protected] 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

Lysozyme in water full (GitHub)
Stable

Lysozyme in water full COMPSs application

Type: COMPSs

Creator: Javier Conejero

Submitter: Raül Sirvent

Deepconsensus for Sequel2/2e subreads

deepconsensus 1.2 snakemake pipeline

This snakemake-based workflow takes in a subreads.bam and results in a deepconsensus.fastq

  • no methylation calls !

The metadata id of the subreads file needs to be: "m[numeric][numeric][numeric].subreads.bam"

Chunking (how many subjobs) and ccs min quality filter can be adjusted in the config.yaml

the checkpoint model for deepconsensus1.2 should be accessible like this: gsutil cp -r gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* ...

Type: Snakemake

Creators: None

Submitter: dan rick

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