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805 Workflows visible to you, out of a total of 878
Anti-Cancer potential of a new Derivative of Caffeic Acid Phenethyl Ester targeting the centrosome - DIA-NN data KNIME processing workflow

KNIME workflow describing the analysis of mass spectrometry dataset related to the publication "Anti-Cancer potential of a new Derivative of Caffeic Acid Phenethyl Ester targeting the centrosome". Workflow was built using the KNIME software container environment, version 4.1.3a, which can be created using "docker pull cfprot/knime:4.1.3a" command in Docker. Please consult Github pages for more information on how to use the ...

Type: KNIME

Creators: Katerina Hanakova, David Potesil

Submitter: David Potesil

DOI: 10.48546/workflowhub.workflow.1309.1

FAIR Statistics Aggregator for DOIs
Stable

Lin_X_NFDI4BIOIMAGE

FAIR Statistics Aggregator for DOIs

Table of Contents

  1. Introduction
  2. Features
  3. Requirements
  4. Installation
  5. Usage
  6. Output
  7. Limitations
  8. License

Introduction

This repository hosts a prototype tool designed to analyze and aggregate FAIR (Findable, Accessible, Interoperable, and Reusable) statistics for a list ...

Type: Python

Creators: None

Submitter: SaibotMagd magd

RDM_system_connector
Deprecated

Lin_X_NFDI4BIOIMAGE

RDM_system_connector

WARNING

This is a proof of concept, it has not been decided whether it will be developed into a fully functional tool. Feedback is therefore essential, especially as it is unclear whether this type of tool is useful at all, and if so, which parts, as the concept consists of many different parts. (source code readme:

Type: Python

Creators: None

Submitter: SaibotMagd magd

Galaxy Workflow for CNV Detection with CNVkit and Conversion to Beacon JSON Using cnv-vcf2json
Stable

This Galaxy workflow streamlines comprehensive copy number variation (CNV) analysis by integrating CNVkit’s robust detection capabilities with an efficient conversion step using cnv-vcf2json to format results into Beacon JSON. Designed for computational biologists and bioinformaticians, the workflow standardizes CNV identification and output formatting to enhance interoperability with Beacon networks. It is specifically optimized for use with mapped BAM files from the EGAD00001008392 synthetic ...

Type: Galaxy

Creators: Khaled Jum'ah, Krzysztof Poterlowicz

Submitter: Khaled Jum'ah

nf-core/metatdenovo

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

Type: Nextflow

Creators: Danilo Di Leo, Emelie Nilsson & Daniel Lundin

Submitter: WorkflowHub Bot

Assembly-Hifi-only-VGP3/main

Contiging Solo:

Generate assembly based on PacBio Hifi Reads.

Inputs

  1. Hifi long reads [fastq]
  2. K-mer database [meryldb]
  3. Genome profile summary generated by Genomescope [txt]
  4. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate.
  5. Genomescope Model Parameters generated by Genomescope [tabular]
  6. Database for busco lineage (recommended: latest)
  7. Busco lineage (recommended: vertebrata)
  8. Name of first assembly
  9. Name of second ...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Assembly-Hifi-Trio-phasing-VGP5/main

Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb]
  5. Paternal hapmer database [meryldb]
  6. Maternal hapmer database [meryldb]
  7. Genome profile summary generated by Genomescope [txt]
  8. Genome model parameters generated by Genomescope [tabular]

...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Use Case 4: Identify the Tissue Activity for a TF based on its Targets

The workflow starts with selecting KLF4 as the search term. Gene sets with set labels containing KLF4 were queried from Enrichr[1]. Identified matching terms from the ENCODE TF ChIP-seq 2015[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ENCODE_TF_ChIP-seq_2015. Identified matching terms from the ChEA 2022[4] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ChEA_2022. Identified ...

Type: Unrecognized workflow type

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1239.2

Use Case 5: Small Molecules to Induce a Biological Process

The workflow starts with selecting Autophagy as the search term. Gene sets with set labels containing Autophagy were queried from Enrichr[1]. Identified matching terms from the MGI Mammalian Phenotype Level 4 2019[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for MGI_Mammalian_Phenotype_Level_4_2019. All the identified gene sets were combined using the union set operation. Reversers and mimickers from over 1 million signatures were identified ...

Type: Unrecognized workflow type

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1240.2

Use Case 6: CFDE Knowledge about a Variant

The workflow starts with selecting chr10:g.3823823G>A as the search term. The closest gene to the variant was found using MyVariant.info[1]. RNA-seq-like LINCS L1000 Signatures[3] which mimick or reverse the the expression of KLF6 were visualized. Median expression of KLF6 was obtained from the GTEx Portal[8] using the portal's API. To visualize the scored tissues, a vertical bar plot was created Fig..

  1. Lelong, S. et al. BioThings SDK: a toolkit for building high-performance data APIs in ...

Type: Unrecognized workflow type

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1241.2

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