How do I download the dataset mentioned in the first paper?
Hello, I am new to this website and I feel a bit stupid and lost. I cannot find the dataset described in the paper “The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug...
View ArticleGPX4 and WWTR1 CRISPR LRT values missing
The CRISPR LRT values for GPX4 and WWTR1 are missing in the Target Discovery Tool. Can these be added? Cheers! 1 post - 1 participant Read full topic
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WGS CN data and functional partial deletions
Hello, I have a question regarding the new CN data released with the DepMap release 24Q2. It appears that functional partial gene deletions are not detected in the WGS/WES derived CN data...
View ArticleHow should I interpret changes in top co-dependencies across different datasets?
Hello everyone, TL;DR: I see different top co-dependencies between the 20Q2 and 24Q2 for the gene CHEK1. I think this might be because the 20Q2 version was calculated using CERES whereas 24Q2 is...
View ArticleSubset analysis not working
I have lists of cell lines loaded in my account and when I now do a ‘Custom Analysis’ and pick a sublist the sublist is ignored and all cell lines are analyzed anyway. If I open the results in Data...
View ArticleHow can the sgRNA in the CRISPRInferredGuideEfficacy file be mapped to the...
In the 24Q2 data release, I would like to find the Model ID for each sgRNA in the CRISPRInferredGuideEfficacy.csv (Data | DepMap Portal). Is there a mapping file available that I can use to obtain the...
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Chronos model's formula
Cannot understand how the formula I circled was derived…Can anyone helps me? thanks![ 1 post - 1 participant Read full topic
View ArticleWhich one of the expression data is proper for machine learning?
Hi, thank you for your effort in launching the newest dataset version 2024Q2. But I’m a little confused about the two kinds of gene expression data: original and batch normalized. If I want to use the...
View ArticleWas the silent mutation removed from the OmicsSomaticMutations.csv in 24Q2?
Hi, Sorry for the frequent question. While checking the 24Q2 dataset, I found that there were no silent mutation labels in the OmicsSomaticMutation.csv file. Although I filtered out the silent...
View Article219 ModelIDs in 23Q4 are not in the 24Q2 release
Dear DepMap team, Would you explain why 219 ModelIDs in the 23Q4 are missing in the new release 24Q2? Best regards, Alice 1 post - 1 participant Read full topic
View Articlecustom gene list download
Hi DepMap, I am trying to download drug screen datasets for some specific genes, but the files appear empty. If I download All genes list it works fine. Thanks! 1 post - 1 participant Read full topic
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ScreenMedianEssentialDepletion pushes off predictability tile
Hello! Just pointing out that the ScreenMedianEssentialDepletion text pushes the predictability table off. The screenshot is for SOX10. Thanks! 1 post - 1 participant Read full topic
View ArticleValues in OmicsCNGene.csv 24Q2 release
Dear DepMap team, Would you please explain why the values in the 24Q2 Omics Gene.csv file are changed (lower) compared to the previous versions such as 23Q2 and 23Q4? I know PureCN was used to...
View ArticleAvailablity of full RNA-seq data for CRISPR screens
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View ArticleVariants reported in OmicsSomaticMutations data
Dear DepMap-Team, I noticed that for a lot of variants in the OmicsSomaticMutations.csv file there is no entry for ModelID. How can I know in which cell line the variant is present? Thank you very...
View ArticleBatch effect removal
Hi DepMap Is it acceptable to use your RNA-seq count data (log2(TPM+1)) without batch effect removing for DEG analysis ? Thank you. 1 post - 1 participant Read full topic
View ArticleRegarding Mutations
Hi, I want to know the usage of ‘Export from mutation table’ under custom downloads tab? Like, how is it different than mutations dataset downloaded under ‘Export from datasets’ under custom downloads...
View ArticleCRISPRGeneEffect vs. ScreenGeneEffect
What is the difference between these 2 files? - I could not see any differences specified in the README file 2 posts - 2 participants Read full topic
View ArticleDifferences of the nubmer of mutations between 23Q2 and 24Q2
Hi, I have a question about the differences in the number of mutations between 23Q2 and 24Q2. For example, when I checked the frequency of mutation in the AARS2 gene at the Jurkat cell line, I found...
View ArticleRunning the DepMap data explorer v2 UI locally
Hi Is the data explorer v2 UI code available somewhere so I can run it locally on my pc and try to play with it to add some of my own features? 1 post - 1 participant Read full topic
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