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821 Workflows visible to you, out of a total of 894
CWL Protein MD Setup tutorial
Stable

Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

Copyright & Licensing

This software has been developed in the [MMB ...

Type: Common Workflow Language

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.279.2

Galaxy workflow demonstrating the usage of EODIE Galaxy Tool
Stable

This workflow demonstrates the usage of EODIE, a toolkit to extract object based timeseries information from Earth Observation data.

EODIE is a toolkit to extract object based timeseries information from Earth Observation data.

The EODIE code can be found on Gitlab .

The goal of EODIE is to ease the extraction of time series information at object level. Today, vast amounts of Earth Observation data are available to the users via for example earth explorer ...

Type: Galaxy

Creator: Anne Fouilloux

Submitter: Anne Fouilloux

DOI: 10.48546/workflowhub.workflow.274.1

Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in CWL
Stable

Common Workflow Language example that illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI). This workflow returns a resulting protein structure and simulated 3D trajectories.

Type: Common Workflow Language

Creator: Genís Bayarri

Submitters: Robin Long, Douglas Lowe

DOI: 10.48546/workflowhub.workflow.29.3

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Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in Galaxy
Work-in-progress

Galaxy workflow example that illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI). This workflow returns a resulting protein structure and simulated 3D trajectories.

Designed for running on the https://dev.usegalaxy.es Galaxy instance.

Type: Galaxy

Creators: None

Submitter: Douglas Lowe

DOI: 10.48546/workflowhub.workflow.194.1

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Cell Lineage in the adult mouse corpus callosum
Stable

Summary

This notebook demonstrates how to recreate lineages published in the paper Live imaging of remyelination in the adult mouse corpus callosum and available at idr0113-bottes-opcclones.

The lineage is created from the metadata associated to the specified image.

To load the data from the Image Data Resource, we use:

Type: Jupyter

Creator: Jean-Marie Burel

Submitter: Jean-Marie Burel

ASPICov
Stable

ASPICov was developed to provide a rapid, reliable and complete analysis of NGS SARS-Cov2 samples to the biologist. This broad application tool allows to process samples from either capture or amplicon strategy and Illumina or Ion Torrent technology. To ensure FAIR data analysis, this Nextflow pipeline follows nf-core guidelines and use Singularity containers.

Availability and Implementation: https://gitlab.com/vtilloy/aspicov

Citation: Valentin Tilloy, Pierre Cuzin, Laura Leroi, Emilie Guérin, ...

Type: Nextflow

Creators: Valentin Tilloy, Pierre Cuzin, Laura Leroi, Patrick Durand, Sophie Alain

Submitter: Valentin Tilloy

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FAIR CRCC - send data
Work-in-progress Tests Not available

Snakemake workflow: FAIR CRCC - send data

Snakemake GitHub actions status

A Snakemake workflow for securely sharing Crypt4GH-encrypted sensitive data from the CRC Cohort ...

Type: Snakemake

Creator: Luca Pireddu

Submitter: Luca Pireddu

polya_liftover
Stable

polya_liftover - sc/snRNAseq Snakemake Workflow

A [Snakemake][sm] workflow for using PolyA_DB and UCSC Liftover with Cellranger.

Some genes are not accurately annotated in the reference genome. Here, we use information provide by the [PolyA_DB v3.2][polya] to update the coordinates, then the [USCS Liftover][liftover] tool to update to a more recent genome. Next, we use [Cellranger][cr] to create the reference and count matrix. Finally, by taking advantage of the integrated [Conda][conda] and ...

Type: Snakemake

Creator: Ryan Patterson-Cross

Submitter: Ryan Patterson-Cross

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RNA-Seq
Stable

RNA-Seq pipeline

Here we provide the tools to perform paired end or single read RNA-Seq analysis including raw data quality control, differential expression (DE) analysis and functional annotation. As input files you may use either zipped fastq-files (.fastq.gz) or mapped read data (.bam files). In case of paired end reads, corresponding fastq files should be named using .R1.fastq.gz and .R2.fastq.gz suffixes.

Pipeline Workflow

All analysis steps are illustrated in the pipeline ...

Type: Bpipe

Creator: Sergi Sayols

Submitter: Sergi Sayols

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ChIP-seq
Stable

ChIP-Seq pipeline

Here we provide the tools to perform paired end or single read ChIP-Seq analysis including raw data quality control, read mapping, peak calling, differential binding analysis and functional annotation. As input files you may use either zipped fastq-files (.fastq.gz) or mapped read data (.bam files). In case of paired end reads, corresponding fastq files should be named using .R1.fastq.gz and .R2.fastq.gz suffixes.

Pipeline Workflow

All analysis steps are illustrated in ...

Type: Bpipe

Creator: Sergi Sayols

Submitter: Sergi Sayols

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