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error in custom analysis
I’m trying to compare the CRISPR dependencies of one cell line vs two other cell lines. It returns an unexpected error. 2 posts - 2 participants Read full topic
View ArticleIC50 unit of measure
Hi, In the file “Drug_sensitivity_AUC_(CTD^2)_subsetted” Are the IC50 values informed in micromolar? If so, what do negative values mean? Was the concentratation range (7.8-2000 nM) the same for all...
View ArticleGDSC or CTD2 data in data explorer?
Hi As always great to have DepMap and the Data Explorer tool! Question - in Data Explorer it seems I’m able to drug screen data just for the PRISM screens (which are great) but not GDSC or CTD2. Is...
View ArticleAvailability of VCF/WGS data for cell line demultiplexing
Hi all, I am working with a single-cell RNA-seq experiment where two cell lines, HT29 (COAD) and KP4 (Pancreas), were multiplexed together before sequencing. The data has been aligned to the GRCh38...
View ArticleTACC3 AO-252 Phase 1A
A2A Pharmaceuticals has a TACC3 inhibitor in phase 1 for ovarian, triple negative and endometrial cancers. Based on complete regressions preclinically, for these indications as well as gastric and...
View ArticleBatch corrected counts data
Is there a batch-corrected version of the counts data, that combines the stranded and unstranded RNA-seq profiles? I see there is a batch-corrected form of the log(TPM+1) counts, so I assume the...
View ArticleReference genome for mutation data
Hi, we are looking at the list of mutations for DU145 cell line ( DepMap ID: ACH-000979) and guessing the position is from hg38 genome, can you please confirm this? Thank you very much in advance! 2...
View ArticleIssue with Drug sensitivity AUC (CTD^2)
Hi, I am encountering an issue while downloading the Drug Sensitivity AUC (CTD^2) file from the custom download section. Specifically, the values in the file do not appear to be AUC scores, as they...
View ArticleDepMap portal cell line mutation,
Hello, What version does the DepMap portal use currently to annotate a mutation in a cancer cell line with the default setting? A couple of cell lines showed a different mutation pattern between cBio...
View ArticleNCI-H854 Oncotree cancer type
Hi, NCI-H854 was annotated as a lung cancer in 2019, but is now annotated as a colorectal cancer model. Was there a documented reason for this change? It is also annotated as being from a primary...
View ArticlePrism compound and cell line count
Hello Community, I´m not sure if this exact question has been asked before. After going through some posts I could not find an answer which is why I´m trying it this way. The main question is: How...
View ArticleHow do we interpret the ssGSEA scores in DepMap?
What do the scores for the ssGSEA mean? Is there a convention (negative vs positive score) and threshold for the ssGSEA scores? Does the score represent the degree to which a particular model...
View ArticleData "PRISM Repurposing Public 24Q2" in Custom Downloads
Sorry I am curious about the data type and source of “PRISM Repurposing Public 24Q2” in Custom Downloads column for that I am presently using it for analysis. My question is what’s the technique of...
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How to Best Analyze DepMap Data for Identifying Cancer Dependencies?
Hey folks, I am new to the DepMap resource & diving into cancer dependency data. Also I have been exploring the dataset but I am a bit overwhelmed with where to start and what tools to use for...
View ArticleSome 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...
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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...
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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
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