CCLE/Depmap License Clarification
Having trouble finding license terms for the following files, and would appreciate support: harmonized_MS_CCLE_Gygi.csv uniprot_hugo_entrez_id_mapping.csv...
View ArticleRNAi equivalent of gene dependency probabilities
Hi DepMap team, I notice that for the CRISPR screens, you have the following downloadable dataset: CRISPRGeneDependency.csv: Gene dependency probability estimates for all models in the integrated gene...
View ArticleCells mistakenly assigned as SCLC
I observed that 3 cells are assigned as SCLC but they are other model type, and one cell has a contamination problem ACH-000727, NCI-H2066 is a Lung squamous cell carcinoma (RRID:CVCL_1520)...
View ArticleMissing data on SOD2 gene expression in 26Q1 and 25Q3
In the expression data (both when accessed through the Custom Downloads feature, and when downloading the complete data file) of at least 26Q1 and 25Q3 Public releases there is no data on expression...
View ArticleValue-free PTEN model projection for DepMap Public 26Q1?
We are assessing whether a public-model study of untreated baseline total PTEN protein is feasible without opening assay matrices. We are not asking for files yet and do not want assay values or...
View ArticleOrganoid dependency data
I tried to find the recently published 3D tumor organoid dependency dataset on the DepMap portal without success. Any guidance would be much appreciated! 1 post - 1 participant Read full topic
View ArticleAbsolute copy number data release
Was OmicsAbsoluteCNGene.csv discontinued after 24Q4? If so, what’s the recommended replacement for absolute copy number data? Thank you! 2 posts - 2 participants Read full topic
View ArticleDiscrepancy between OmicsAbsoluteCNGene and OmicsAbsoluteCNSegmentsProfile
Hi, I was looking at OmicsAbsoluteCNGene values (24Q4) for the gene DCC on chromosome 18q, in relation to the segment value in OmicsAbsoluteCNSegmentsProfile (also 24Q4). For cell line ACH‑000679...
View ArticleTSS_RRBS_Methylation_Data
I have noticed that some genes are not available in any of the methylation datasets (CCLE_RRBS_TSS_1kb_20180614.txt, CCLE_RRBS_TSS_CpG_clusters_20180614.txt), but seem to be available through the...
View Article26Q1 OmicsCNGeneWGS.csv normalization
In the 26Q1 OmicsCNGeneWGS.csv release, what is the reported linear copy number ratio normalized against? Does a ratio of ~1.0 incorporate that specific cell line’s own ploidy (e.g. a value of ~1.0...
View ArticleHow should CRISPRInferredModelEfficacy.csv identifiers be mapped in DepMap...
How should CRISPRInferredModelEfficacy.csv identifiers be mapped in DepMap Public 26Q1? I am working with the DepMap Public 26Q1 files and need to map CRISPRInferredModelEfficacy.csv reproducibly to...
View ArticleProvide an open endpoint for latest version retrieval
With the latest changes to the DepMap portal, to add a captcha layer, it is now no-longer possible to programmatically download files. The bulk download option mentioned in the captcha also redirects...
View ArticleBulk download gene effect z-scores
To whom it may concern, I want to download the gene effect z-scores for all genes in all cell lines. depmap.org DepMap — Verification depmap.org DepMap — Verification … Is there a bulk download option...
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Error when downloading files using custom download
Hi, I am getting the following error when trying to download drug sensitivity and crispr data using custom download for particular model. Please help me resolving this issue. 1 post - 1 participant...
View ArticleRNA pipeline reference availability
I am trying to run the DepMap Omics RNA pipeline on my own data. The pipeline is available here but the genome reference files in the ‘ccleparams’ bucket are not accessible; specifically I’m getting a...
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Keep getting this error when downloading Cell Line data through custom downloads
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View ArticleRegarding gene expression and gene effect score
Regarding gene expression and gene effect score, I have found that the mRNA expression of some genes may be unrelated to or inversely proportional to the gene effect score. That is, the greater the...
View ArticleHelp with understanding DepMap Cell line summary
When I type in a cell line, on the right there is a column Header that says “Molecular Subtypes”. Under this it will often say “Level 0”, and under that it might say “CDKN2A-Lof”. What does Level 0...
View ArticleAneuploidy score version in DepMap
Hi, A year ago Ive done an analysis using the aneuploidy score in the data explorer. Now I wanted to recreate this analysis however the data wasnt there anymore. When looking I found a different...
View ArticleStatistical test used in Custom Analysis (2-class comparison)
I’ve used DepMap’s Custom Analysis 2-class comparison feature to compare three data types between two groups of cell lines : CRISPR Chronos scores Gene expression Metabolite abundance I have two...
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