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src/pages/outreach/Omics Tools Seminar Series: ARCHS4 2025-02-27.md renamed to src/pages/outreach/Omics Tools Webinar Series: ARCHS4 2025-02-27.md

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image: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/archs4-feb-2025-4.png
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layout: '@/layouts/Outreach.astro'
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link: https://mountsinai.zoom.us/webinar/register/WN_ZXBJyN0SRuCj5LaYoGeXuw#/registration
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short_description: The seminar featured ARCHS4, a resource that provides access
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short_description: The webinar featured ARCHS, a resource that provides access
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to gene and transcript counts uniformly processed from all the human and mouse RNA-seq
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experiments deposited by the community in the NCBI Gene Expression Omnibus (GEO).
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start_date: '2025-02-27T14:00:00-05:00'
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tags: '["workshop"]'
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title: 'Omics Tools Seminar Series: ARCHS4'
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title: 'Omics Tools Webinar Series: ARCHS4'
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---
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The seminar featured ARCHS4, a resource that provides access to gene and transcript counts uniformly processed from all the human and mouse RNA-seq experiments deposited by the community in the NCBI Gene Expression Omnibus (GEO).
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The webinar featured [ARCHS4](https://maayanlab.cloud/archs4/), a resource that provides access to gene and transcript counts uniformly processed from all the human and mouse RNA-seq experiments deposited by the community in the NCBI Gene Expression Omnibus (GEO). Watch recording [here](https://www.youtube.com/watch?v=BSz4XWFmfkg).

‎src/pages/outreach/Omics Tools Webinar Series: GeneSetCart 2025-01-23.md‎

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---
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active: true
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cfde_specific: true
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dcc:
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- LINCS
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start_date: '2025-01-23T14:00:00-05:00'
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end_date: '2025-01-23T15:00:00-05:00'
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featured: true
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image: /img/genesetcart_webinar.png
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layout: '@/layouts/Outreach.astro'
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link: https://mountsinai.zoom.us/webinar/register/WN_ZXBJyN0SRuCj5LaYoGeXuw#/registration
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short_description: In this lecture, Giacomo Marino, a Bioinformatics Software Engineer in the Ma'ayan Lab at the Icahn School of Medicine at Mount Sinai, describes a new platform for assembling, augmenting, combining, visualizing, and analyzing gene sets. The platform utilizes LLMs to form hypotheses from datasets produced by NIH Common Fund programs.
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tags: '["workshop"]'
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title: 'Omics Tools Webinar Series: GeneSetCart
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'
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---
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Converting multi-omics datasets into gene sets facilitates data integration that leads to knowledge discovery. Although there are tools developed to analyze gene sets, only few offer the management of gene sets from multiple sources. GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets, all in one place. GeneSetCart supports the upload of single or multiple gene sets, as well as fetching gene sets by searching PubMed for genes co-mentioned with terms in publications. Venn diagrams, heatmaps, UMAP, SuperVenn diagrams, and UpSet plots can visualize the gene sets in a GeneSetCart session to summarize the similarity and overlap among the sets. Users of GeneSetCart can also perform enrichment analysis on their assembled gene sets with external tools. All gene sets in a session can be saved to a user account for reanalysis and sharing with collaborators. GeneSetCart has a gene-set-library crossing feature that enables analysis of gene sets created from several NIH Common Fund programs. For the top overlapping sets from pairs of programs, a large language model (LLM) is prompted to propose possible reasons for the high overlap. Using this feature, two use cases are presented. In addition, users of GeneSetCart can produce publication-ready reports from their uploaded sets. Text in these reports is also assisted with an LLM. Overall, GeneSetCart is a useful resource for biologists without programming expertise to facilitate data integration for hypothesis generation.

‎src/pages/publications/DOI:10.1101-2025.02.04.636535.md‎

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authors: John Erol Evangelista, Daniel J.B. Clarke, Zhuorui Xie, Stephanie Olaiya, Heesu Kim, Giacomo B. Marino, Anna Byrd, Shivaramakrishna Srinivasan, Sumana Srinivasan, Mano R. Maurya, Sherry L. Jenkins, Andrew D. Lutsky, Lucas Sasaya, Alexander Lachmann, Nasheath Ahmed, Ido Diamant, Ethan Sanchez, Srinivasan Ramachandran, Shankar Subramaniam, Avi Ma’ayan
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carousel: false
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carousel_link: https://www.biorxiv.org/content/10.1101/2025.02.04.636535v1
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carousel_description: LEARN MORE ABOUT THE **CFDE WORKBENCH** BY READING THE PREPRINT ON BIORXIV
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image: /img/workbench.png
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centers:
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- DRC
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doi: doi.org/10.1101/2025.02.04.636535
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featured: false
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journal: bioRxiv
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landmark: true
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layout: '@/layouts/Publication.astro'
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title: ' The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs'
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title: 'The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs'
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year: 2025
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---

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