Clarifying the Criteria for Identifying Oncogenic Alterations in DepMap Cell...
Hi! I’ve been exploring the DepMap portal, specifically the page for a cell line (e.g., ACH-000328), and I’m intrigued by the section on “Oncogenic Alterations.” In my attempt to replicate this data...
View Articlegot forbidden 403
Hello, I was checking manually a list of 48 genes, when I got to 42 I saw the forbidden 403 message and got blocked. I was not running code on the website, just checking if genes were strongly...
View ArticleAvailability of WGS or WXS data for cell lines
Hello, Neither WGS nor WXS data is on DepMap for 15 of the cell lines I need even though mutation status and other information is available for these cell lines. Is there a way for my lab to request...
View ArticleAPI endpoints for perturbation and/or expression?
Going to an example gene page: TACO1 DepMap Gene Summary, we see plots of data for perturbation and characterization. Are there any publicly available API endpoints to fetch this data? Either the raw...
View ArticleCan a threshold be set in the gene effect？
Can a threshold be set in the gene effect, below which the gene is considered an essential gene in the cell line? 1 post - 1 participant Read full topic
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Is there a threshold in Drug Sensitivity AUC?
Is there a threshold in Drug Sensitivity AUC, below which it is considered that the drug has an impact on cell line proliferation? which threshold? Similarly, does a threshold also exist in the PRISM...
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Mutation missing for line NCI-H2126
Hi team, I downloaded the CCLE_mutations.csv file for my research study, I’m interested in cell lines STK11 mutated. I found out from my literature studies that the line ACH-000785 (NCI-H2126) is...
View ArticleHow to go from unvalidated cell line (e.g. K562) to a DepMap ID (ACH-000551)?
I am trying to think about how to go from a cell line name (e.g. K562) to a DepMap ID (ACH-000551) for thousands of cell lines in a CSV file. How can one accomplish that? 2 posts - 1 participant Read...
View ArticleConverting DepMap ID to Cellosaurus ID
Which of the downloadable CSV files will enable to converting a cell line’s DepMap ID to Cellosaurus ID? 2 posts - 1 participant Read full topic
View ArticleQuestion about how to interpret CHRONOS gene effect scores
I think I’m still struggling to understand how to interpret CHRONOS gene effect scores. For my gene of interest, in my cancer type of interest the average gene effect score is about -0.9, while for...
View ArticleIs it possible to check which CRISPR sgRNA library was used to screen each...
I am trying to determine which library (e.g. Avana, KY or Humagne) is used for a particular cell line. Is this data available? 1 post - 1 participant Read full topic
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Pre-computed association: Proteomics
Dear Team, I am wondering why preteomics association is not existed in pre-computed? Is there any way to identify genome-wide association with Proteomics data for gene of interest? Thanks. Shicheng 2...
View ArticleEWSR1 fusion cancers
I would like to analyze drug compound sensitivity according to presence or absence of a fusion event involving EWSR1. How can I do that easily? Thanks. David 1 post - 1 participant Read full topic
View ArticleCCLE_expression data values are different
Hello, I was wondering why in Quarterly released CCLE_expression data have different values for the same gene? I have checked CCLE_expression from 22Q1 and 19Q2. I also checked CCLE_RNAseq_reads.csv,...
View ArticleRe-distribution of the CCLE data (Licensing)
Hey everyone, I was wondering about the licensing of DepMap, especially CCLE. Am I allowed to re-distribute the dataset on another website? Best, Judith 1 post - 1 participant Read full topic
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About Depmap page footer
Hi Phil! Just a heads up that the footer at the bottom of depmap-homepage seems weirdly sized (and the page might want a header title). (Love the home page!) Cheers, J 1 post - 1 participant Read full...
View ArticleSearch for targets within selected cell line group
Hi there, I have just started using the tool. I am interested in looking spefically at gastro/ oesophageal lines. I managed to create a cell line group and select all the lines, which I can then...
View ArticleCategorization of Cell Lines by DepMap Release Date
Hi all, I’m trying to track the order of the addition of new cell lines to DepMap. I’d like to know what was the first release that included CRISPR screen data for a particular cell line, for the...
View ArticleBam files from RNA seq data ?
Is there a way to get Bam files from the RNA seq data of cell lines? 2 posts - 2 participants Read full topic
View Article23Q4 ACH-000190 HDMYZ is incorrectly annotated as AML
Hello, Could you please update the 23Q4 annotation for the ACH-000190 HDMYZ cell line? In the 23Q4 DepMap release, HDMYZ is annotated as “Myeloid/AML”. In DSMZ and Cellosaurus the cell type for HDMYZ...
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