Hands-On Workshop: Data, Tools, and Workflows for CMap analysis | LINCS Virtual Symposium 2020

LINCS Virtual Symposium | November 19-20, 2020
Session III: Hands-On Workshop/Poster Session
Workshop Topic: LINCS Transcriptomics: Data, Tools, and Workflows for Connectivity Map analysis
Presenters: Rajiv Narayan, Ted Natoli, Anup Jonchhe and Jacob Asiedu (Broad Transcriptomics)
This workshop focuses on tools and datasets from the Connectivity Map (CMap) project, part of the LINCS Center for Transcriptomics at the Broad Institute. The overarching concept of CMap is to use mRNA signatures of cell state to link genes, drugs, and diseases. This presentation goes over the newest LINCS 2020 data release, now available at clue.io and in Google BigQuery. The CMap team demos how to access the data using clue.io/query, as well as using the Python-based package cmapBQ, which is designed to extract target datasets from Google BigQuery. Interesting subsets of the latest data release that may be useful for analysis are also covered, including compounds profiled at dose, CRISPR signatures, hematopoietic cell lines, and ligands.
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