A missing cell line in hotspot mutation table
Hello DepMap team, I think you might missed ACH-000839 (SCABER) in the “OmicsSomaticMutationsMatrixHotspot.csv”, whereas this cell line exists in “OmicsSomaticMutationsMatrixDamaging.csv”. This one...
View ArticleHome Page Compound Link Broken
On the portal’s home page is Dabrafenib compound overview which leads to 404 Not Found. 4 posts - 2 participants Read full topic
View ArticleRepurposing Hub Broken Link
On a compound overview, there is Metadata from the Repurposing Hub which never loads when clicked. 2 posts - 2 participants Read full topic
View ArticleData Removed? Navitoclax single agent data
As of yesterday, there were several data sets for Navitoclax as a single agent (both Sanger data sets, IC50 and AUC), but today the option to choose navitoclax as a single agent is not available...
View ArticleDownloading "Likely LOF" data
Hi! Is there a way to download the “Likely LOF” data in Custom Downloads? I am interested in downloading this data for some genes of interest across all cell lines. However, I am not seeing an easy...
View ArticleDepMap User Group
Dear All, DepMap datasets are invaluable and I believe we need an active user group to have Weekly/Monthly meetings to share/exchange our knowledge and experience. If I get 5 positive responses I will...
View ArticleDownload profile data
Thank you very much for the database you developed. For a given gene such as TP53, how do we calculate the Top Co-dependencies? Is it by comparing the correlation of differential genes after two genes...
View ArticleNon-Cancerous Cell Lines
Hello, Having non-cancerous cell lines corresponding to each cancer cell line holds immense potential and would significantly enhance research and therapeutic advancements in the field. Best, Saed 3...
View ArticleCopy number variation
Hello, I’m trying to get a copy number mutational signature. I saw that I used ABSOLUTE method in 2018. Is it the same way you use it now? If it’s different, I wonder what you use. And can I get a...
View ArticleCCLE cell line RNA-Seq raw read counts
Where can I access the cell lines RNA-Seq raw read counts? I don’t see it available from the download portal. thanks! 1 post - 1 participant Read full topic
View ArticleOmicsSomaticMutations 23Q4 missing driver/gof/lof columns
Some columns described in https://storage.googleapis.com/shared-portal-files/Tools/[DMC%20Communication]%2022Q4%20Mutation%20Pipeline%20Update.pdf are missing, e.g. Driver, LikelyDriver, LikelyGoF,...
View ArticleNon-Cancerous cases have Primary or Metastatic labels
Hi, How come some of Non-Cancerous cases have Primary or Metastatic labels? PrimaryOrMetastasis,OncotreePrimaryDisease.Count Primary,Non-Cancerous,14 Metastatic,Non-Cancerous,4 Thanks, Saed 1 post - 1...
View ArticleCell Line Selector Visualization
I think it’s really cool that you can make a custom link to see where certain cell lines of interest occur on the box graphs on pages like the “Expression Public” or “Copy Number” for genes. However,...
View ArticleAbsence of RPE1 cell line information in DepMap 23Q2
Dear DepMap community, Greetings, I have a question about the cell-line information in the DepMap 23Q2 dataset (i.e., CCLE dataset). When I checked the model.csv file for tracking cell-line...
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Shrinkage of betas to EffectSize / PosteriorMean
Hi DepMap team, Seeking some clarification over the EffectSize which is referred to as “PosteriorMean” in one of the previous posts and in R package cdsrmodels. I am looking at a rather strange...
View Articleperturbation error
When I click pertubation, there is an an internal error occurred and I can not continue search. 1 post - 1 participant Read full topic
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How to find telomere content in Data Explorer?
Hi! Based on the announcement on 9/21/2021, telomere content has been added to Data Explorer (see attached). I’m interested in knowing how I can find that tab in Data Explorer. 1 post - 1 participant...
View ArticleSomatic mutations: coverage for homozygote reference samples
Hi ! are you planning to add coverage information for the somatic mutations and the homozygote reference samples ? In the OmicsSomaticMutations.csv from DepMap Public 23Q4, coverage is only available...
View ArticleClarifying the Criteria for Identifying Oncogenic Alterations in DepMap Cell...
Hello, I am currently conducting research using the DepMap portal, particularly interested in the “Oncogenic Alterations” displayed on cell line pages, such as ACH-000328. I am seeking clarification...
View ArticleI got the forbidden 403 screen
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...
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