How can I access genomic files?
The DepMap project was built off of the original CCLE project and continues to grow and generate new data. Genomic data from CCLE and DepMap can be accessed in separate way: CCLE Legacy files:...
View ArticleMicroRNA codes
How can i know the microRNA codes in the downloaded data from DepMap stands for which microRNA 1 post - 1 participant Read full topic
View ArticleDemMap's call for cancer models
Hello everyone, I wanted to clear a confusion regarding depmap’s call for cancer models initiative. As it seems an open call to submit cancer models, i was wondering, if the characterization and...
View ArticleAneuploidy score
Hi all, In the previous Depmap platform there use to be the aneuplidy score dataset. I cannot find it any longer. Could you help me, please? 1 post - 1 participant Read full topic
View ArticleCRISPR Dual-Knockout screening
Hi, I have a simple question about the CRISPR Dual-Knockout (CDKO) screening in the DepMap portal. In this paper, the authors mentioned that ‘DepMap also consists of drug-gene and gene-gene...
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OmicsSomaticMutations.csv, multiple mutation rows of the same cell-line and...
Just want to reiterate how thankful I am for all the helpful and quick responses I have had about this dataset. I had a question regarding the OmicsSomaticMutations dataset that is in MAF format. I am...
View ArticleCell line annotations
hello,I would like to know if the DepMap 24Q4 data includes files with detailed annotations for cell lines,thank you for your help 2 posts - 2 participants Read full topic
View ArticleClarification on Negative Values in Log-Transformed Gene Expression Data
I am working with the DepMap expression datasets, and I have a question regarding the log-transformed values in the OmicsExpressionProteinCodingGenesTPMLogp1.csv file. As per the dataset...
View ArticleConflicting values in CN data
Using Copy Number Public 24Q4 data, shouldn’t these be the linear (non-log-transformed) versions of Copy Number Public 24Q4 (Log2 transformed) ? I’ve loaded both linear and log2-transformed data in...
View ArticleGDSC1 and GDSC2 AUC data
Hello, Is there a method to find the original AUC data from these datasets? Rather being in terms of 0-1, I’m looking for a resource that can provide these AUC numbers in terms of dosage (uM) * hours....
View ArticleHow to access/run correlations on proteomics data
Hi I have been trying to correlate drug sensitivity with RPPA expression of ERBB2_py1248 across cell lines. I used to do this by selecting custom analysis, then gene ERBB2, then I could select...
View ArticleDepmap.org portal latency
Hello DepMap team, Starting around the time of the 24Q4 data release, I noticed the public portal slowed down dramatically. Today it’s timing out (see below). The issue doesn’t seem to be localized to...
View ArticleWhat happened to the chromosome arm level copy number data
Hi The arm-level copy number data used to be in the Data Explorer, but now I can not find it anywhere, even in the download section. Can you tell me what happened to it? 3 posts - 2 participants Read...
View ArticleOmic signatures discrepancies
Hi DepMap team, I am looking at features like Aneuploidy, WGD etc in the OmicsSignatures.csv files - between 24Q2 and 24Q4 version. There are some cell lines that show discordant values and some that...
View Article"Request for Academic Lab Source Information
Hi, for the cell lines listed with “academic lab” as the source, could we get more information about which specific lab they came from? Thank you! 1 post - 1 participant Read full topic
View ArticleIs the raw RNAseq available for download from cells released after 2019?
Hello, I am looking for RNAseq data for: NCCIT Tera2 SHSY5Y I see the processed gene counts have been uploaded to the portal, but I cannot find the raw RNAseq files for my own analysis. Previous posts...
View ArticleWhat exactly is the SegmentMean in OmicsCNSegmentsProfile.csv?
Hi DepMap team, First of all, thank you very much for your great contribution to the scientific community. I am writing here because I have a doubt regarding the OmicsCNSegmentsProfile.csv file. I am...
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Preferential Essential Genes View Missing - Portal Slow
Hi, a couple of days ago, I was able to view the Top 10 Preferential Gene list. Now if I select certain cell lines, the view is gone. I can no longer download the CRISPR data for individual genes....
View ArticlePhospho-Proteomics data accessibility issue
Dear DepMap Team, Couple of weeks ago, I was able to access and download phospho-proteomics data from the DepMap interface, for classical signalling nodes, such as EGFR, AKT, MAPK… etc for which the...
View ArticleInvestigate the expression level of a gene in defined groups
I would like to know how to use data explorer to make a plot of Gene A expression between high Gene B expression and low Gene B expression. 1 post - 1 participant Read full topic
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