ReproTox-KG
FEATURED

ReproTox-KG

To further characterize associations between small molecule compounds and their potential to induce specific birth abnormalities, we gathered knowledge from multiple sources to construct a reproductive toxicity Knowledge Graph (ReproTox-KG) with a focus on associations between birth defects, drugs, and genes.
ReproTox-KG
Playbook Workflow Builder
FEATURED

Playbook Workflow Builder

The Playbook Workflow Builder (PWB) is a web-based platform that facilitates knowledge resolution by enabling users to traverse an ever-growing network of input datasets, semantically annotated API endpoints, and data visualization tools. Via a user-friendly user-interface, workflows can be constructed from these building-blocks without technical expertise. The output of these workflows is provided as reports containing textual descriptions, interactive figures, and downloadable tables.
Playbook Workflow Builder
Standard RNA-seq Processing Pipelines
FEATURED

Standard RNA-seq Processing Pipelines

The CFDE RNA-seq Pipeline Harmonization partnership is a collaboration between multiple DCCs (GTEx, UDN, KF, HuBMAP, SPARC, MoTrPAC) to update their RNA-seq pipelines across the DCCs with a revised version of the STAR RNA-seq aligner. The goal is to enable uniform alignment to a reference genome by reprocessing all the existing accessible bulk-tissue RNA-seq datasets.
Standard RNA-seq Processing Pipelines
ReproTox-KG
FEATURED

ReproTox-KG

To further characterize associations between small molecule compounds and their potential to induce specific birth abnormalities, we gathered knowledge from multiple sources to construct a reproductive toxicity Knowledge Graph (ReproTox-KG) with a focus on associations between birth defects, drugs, and genes.
ReproTox-KG
Playbook Workflow Builder
FEATURED

Playbook Workflow Builder

The Playbook Workflow Builder (PWB) is a web-based platform that facilitates knowledge resolution by enabling users to traverse an ever-growing network of input datasets, semantically annotated API endpoints, and data visualization tools. Via a user-friendly user-interface, workflows can be constructed from these building-blocks without technical expertise. The output of these workflows is provided as reports containing textual descriptions, interactive figures, and downloadable tables.
Playbook Workflow Builder
Standard RNA-seq Processing Pipelines
FEATURED

Standard RNA-seq Processing Pipelines

The CFDE RNA-seq Pipeline Harmonization partnership is a collaboration between multiple DCCs (GTEx, UDN, KF, HuBMAP, SPARC, MoTrPAC) to update their RNA-seq pipelines across the DCCs with a revised version of the STAR RNA-seq aligner. The goal is to enable uniform alignment to a reference genome by reprocessing all the existing accessible bulk-tissue RNA-seq datasets.
Standard RNA-seq Processing Pipelines
ReproTox-KG
FEATURED

ReproTox-KG

To further characterize associations between small molecule compounds and their potential to induce specific birth abnormalities, we gathered knowledge from multiple sources to construct a reproductive toxicity Knowledge Graph (ReproTox-KG) with a focus on associations between birth defects, drugs, and genes.
ReproTox-KG
Playbook Workflow Builder
FEATURED

Playbook Workflow Builder

The Playbook Workflow Builder (PWB) is a web-based platform that facilitates knowledge resolution by enabling users to traverse an ever-growing network of input datasets, semantically annotated API endpoints, and data visualization tools. Via a user-friendly user-interface, workflows can be constructed from these building-blocks without technical expertise. The output of these workflows is provided as reports containing textual descriptions, interactive figures, and downloadable tables.
Playbook Workflow Builder
Standard RNA-seq Processing Pipelines
FEATURED

Standard RNA-seq Processing Pipelines

The CFDE RNA-seq Pipeline Harmonization partnership is a collaboration between multiple DCCs (GTEx, UDN, KF, HuBMAP, SPARC, MoTrPAC) to update their RNA-seq pipelines across the DCCs with a revised version of the STAR RNA-seq aligner. The goal is to enable uniform alignment to a reference genome by reprocessing all the existing accessible bulk-tissue RNA-seq datasets.
Standard RNA-seq Processing Pipelines

ALL TOOLS AND WORKFLOWS

Explore different tools and workflows that utilizes data from different CFDE participating programs

FAIRshake

FAIRshake

Toolkit to evaluate the FAIRness of research digital resources
FAIRshake
GDLPA

GDLPA

Query 53 gene-centric, 18 variant-centric, and 19 drug-centric repositories
GDLPA
ReproTox-KG

ReproTox-KG

Toxicology knowledge graph for structural birth defects
ReproTox-KG
Data Distillery Knowledge Graph

Data Distillery Knowledge Graph

KG database represents interrelated biomedical ontologies and vocabularies
Data Distillery Knowledge Graph
Playbook Workflow Builder

Playbook Workflow Builder

Web-based platform to construct biomedical workflows
Playbook Workflow Builder
Standard RNA-seq Processing Pipelines

Standard RNA-seq Processing Pipelines

Revised STAR RNA-seq aligner to update RNA-seq pipelines across CF programs
Standard RNA-seq Processing Pipelines