Some files cannot be downloaded!
Hi, When trying to download, ie. secondary-screen-dose-response-curve-parameters.csv, the Google Cloud Storage throws and error and the data cannot be downloaded. Here is the link the download button...
View ArticleHow is 'Haematopoietic And Lymphoid' coming as enriched lineages but are...
For some targets like MERTK and CLDN18 the front end shows ‘Haematopoietic And Lymphoid’ as enriched lineage for CRISPR and RNAi data. Considering the lineage enrichment is calculated from the lineage...
View ArticleClik here to view.
Error in Custom Analysis: Omics Signatures Public
Hi - I’ve been using the custom analysis tools without problem for other datasets but doesn’t seem to work for most variables in the Omics Signatures Public. So WGD status, aneuploidy score etc can’t...
View ArticleClik here to view.
PureCN Custom Analysis error
Hi there, There seems to be an issue when one attempts Pearson correlation with Omics Signatures derived from PureCN (WGD, CIN, LOHFraction) and CRISPR or RNAi screen sensitivities. 1 post - 1...
View ArticleDepMap Data – Exploring Relevance Beyond Oncology
Hi everyone, I’m part of Clearfork Academy, a youth mental health academy working with teens navigating emotional and behavioral health challenges. While our work is outside the typical scope of...
View ArticleData after CRISPR-Cas9 screening
Hi, thank you for providing the valuable dataset about the CRISPR-Cas9 screening. I have a simple question about the future dataset. Do you plan to add the omics data, like CCLE, after CRISPR...
View ArticleRandom forest code
Hi Phil, Simone, DepMap team, I’m interested in running the code underlying the Predictability tabs, which predicts dependency scores from baseline omics. I found the methodology preprint via the...
View ArticleCannot share reports
When I click share button in the reports, its not responding. I’m using Chrome and even when I use Edge the bug remains 1 post - 1 participant Read full topic
View ArticleDrug-Target validation using CRISPR and PRISM repurposing dataset
Hello, i am working on validating Drug-target screens to validate the hypothesis that the drug is inhibiting the gene product by examining that the gene ko and the drug have similar signatures...
View ArticleRegarding CRISPR data for H69
Hello, I am seeing an issue regarding the CRISPR data for small cell line neuroendocine data sets. Previously, i found CRISPR score for NCI-H69, now with the new 24Q4+ i am unable to get any CRISPR...
View ArticleBAM files from RNA seq
I am interested in analyzing transcript splicing, which requires the RNA-seq alignment (BAM) files for the cancer cell lines used in DepMap. I was wondering if these are available through DepMap or...
View ArticleHow to compare essential genes in several cell lines of certain lineage at once?
I need to look through a certain cell line lineage for all top essential genes, for future CRISPR for potential slicing and silencing. For instance, I need all head and neck cell lines, and I’m...
View ArticleCan not click on CpG Methylation datasets
Hello, I am unable to access CpG Methylation datasets for cell lines as it currently isn’t possible to click on the links for the data sets. This issue seems to be present on all cell lines and...
View ArticleQuestion about the naming rule for drugs in Custom Downloads data
Greeting, We have a certain question about the naming rule for drugs in Custom Downloads data. Since there are data from different sources and your team has formated them into fixed formats, we wonder...
View ArticleWGS data access
Hi, Is it possible to access WGS data (FASTQ or BAM files) for specific cell lines from the database? Thanks in advance! 1 post - 1 participant Read full topic
View ArticleAccess to unfiltered cell line VCF files?
How can we access the unfiltered VCF files for the cell lines containing both coding and non-coding variants? 1 post - 1 participant Read full topic
View ArticleClik here to view.
Announcing the 25Q2 Release
25Q2 Public DepMap Release Notes In this release, we have added new CRISPR and Omics data, more WGS data for lines that previously had WES and important updates to our Omics and CRISPR pipelines....
View ArticleAntibiotic doses?
Is there a listing of antibiotic dose used for selection for each of the cell lines in DepMap anywhere? 1 post - 1 participant Read full topic
View ArticleClik here to view.
cell line selector loading......
When I use the Cell Line Selector, the “Data type” in the “Add a data column” section keeps showing “loading” and has remained this way for over a week. How can I resolve this issue? 2 posts - 2...
View Articlecomparison between raw counts and log TPM values
Hello there, I downloaded first the log TPM values and plotted them for a specific gene and found that it is expressed. Then, I have to use another normalization method and downloaded the raw counts....
View Article