Workflows

What is a Workflow?
793 Workflows visible to you, out of a total of 868

A file was first uploaded. The file was parsed as a gene count matrix. Significantly over-expressed genes when compared to tissue expression in GTEx[1] were identified. RNA-seq-like LINCS L1000 Signatures[3] which mimick or reverse the the expression of IMP3 were visualized. Drugs which down-regulate the expression of IMP3 were identified from the RNA-seq-like LINCS L1000 Chemical Perturbagens[3]. Genes which down-regulate the expression of IMP3 were identified from the RNA-seq-like LINCS L1000 ...

Type: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1246.1

The workflow starts with selecting RPE as the search term. For the given gene ID (SYMBOL), StringDB PPI was extracted using their API[1]. For the Given StringDB PPI, the list of nodes (Gene Set) is generated. For the Given StringDB PPI, the list of nodes (GeneSet) is generated. Reversers and mimickers from over 1 million signatures were identified using SigCom LINCS[2]. The gene set was submitted to Enrichr[4]. The gene set was then searched in the Metabolomics Workbench[5] to identify relevant ...

Type: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1245.1

The workflow starts with a gene set created from Example gene set. CTD is applied which diffuses through all nodes in STRING[1] to identify nodes that are "guilty by association" and highly connected to the initial gene set of interest[2][3]. A list of Highly Connected Genes was obtained from the CTD output. A list of Guilty By Association Genes was obtained from the CTD output.

  1. Szklarczyk, D. et al. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic ...

Type: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1244.1

The workflow starts with selecting chr2:g.39417578C>G as the search term. The closest gene to the variant was found using MyVariant.info[1]. Gene expression in tumors for CDKL4 were queried from the Open Pediatric Cancer Atlas API[3]. Median expression of CDKL4 was obtained from the GTEx Portal[4] using the portal's API. To visualize the level of expression across tumor gene expression, a bar plot was created Fig..

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

Type: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1243.1

The workflow starts with selecting KLF6 as the search term. RNA-seq-like LINCS L1000 Signatures[1] which mimick or reverse the the expression of KLF6 were visualized. Median expression of KLF6 was obtained from the GTEx Portal[6] using the portal's API. To visualize the scored tissues, a vertical bar plot was created Fig..

  1. Evangelista, J. E. et al. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Research vol. 50 W697–W709 (2022). ...

Type: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1242.1

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: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1241.1

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: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1240.1

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: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1239.1

The workflow starts with selecting atrial fibrillation as the search term. The workflow starts with selecting Ibrutinib as the search term. Gene sets with set labels containing atrial fibrillation were queried from Enrichr[1]. Identified matching terms from the MGI Mammalian Phenotype Level 4 2021[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for MGI_Mammalian_Phenotype_Level_4_2021. A consensus gene set was created by only retaining genes ...

Type: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1238.1

The workflow starts with selecting Inflammation as the search term. The workflow starts with selecting Penicillin as the search term. The workflow starts with selecting Cortisol as the search term. Gene sets with set labels containing Inflammation were queried from Enrichr[1]. Identified matching terms from the GWAS Catalog 2019[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for GWAS_Catalog_2019. All the identified gene sets were combined ...

Type: Playbook Workflow Builder Workflow

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1237.2

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