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.
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.
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.
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.
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.
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.
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.
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.
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.
ALL TOOLS AND WORKFLOWS
Explore different tools and workflows that utilizes data from different CFDE participating programs
@CFDE Workbench 2024
The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.
The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.
@CFDE Workbench 2024