HPV status of HNSCC
I am trying to find HPV status for the head and neck squamous cell carcinoma models (HNSCC). I don’t see this information in the Models.csv. Is it stored somewhere else? Thanks! 1 post - 1 participant...
View ArticleDetermining Copy Number Alterations for Genes/, as boolean, in DepMap Public...
I am using “DepMap Public 22Q2 Primary Files”. I have a list of a few hundred genes. For each gene I want to determine whether it has a copy number deletion or not. Also, for each gene I want to...
View ArticleRNA-seq paired with CRISPR screen data?
Is the RNA-seq data from “OmicsExpressionProteinCodingGenesTPMLogp1.csv” paired with the CRISPR essentiality data from “CRISPRGeneDependency.csv” and “CRISPRGeneEffect.csv”? i.e. was the same group of...
View Article9-ING-41 repurposing hub data
Hi, Link: 9-ING-41 DepMap Compound Summary 9-ING-41 appears to have been screened but the data from the repurposing hub doesn’t load. Is this data available? Thanks. 1 post - 1 participant Read full...
View ArticleThe meaning of AUC values greater than 1 in the PRISM secondary screen
Dear developers of DepMap, I am currently utilizing the AUC values from secondary screening in the PRISM database for modeling. In the paper by Corsello at 2020, AUC values were described as ranging...
View ArticleData issue with PRISM drug repurposing dataset
Hi, I’ve been analyzing compound screening data from the PRISM Repurposing Secondary Screen and have encountered a potential data or technical artifact. For example, with the compound SN38, I noticed...
View ArticleHow to find a specific analysis
I want to find information on RESISTANT breast cancer cells against two specific compounds. Have been playing with the program a bit and I really do not get how to filter for cells that show a...
View ArticleExtracting AUC Data for Drug-Cell Line Combinations from CTRP CTD^2 Dataset
I am using the data “CTRP CTD^2 All Files”, contained in CTRPv2.0_2015_ctd2_ExpandedDataset.zip. I am trying to figure out for each combination of drug and cell line what the AUC was. Please how can I...
View ArticleHow to mapping the sample IDs in the RNA-Seq RSEM count file to the Model...
In 23Q4 data release, I found the row IDs in the OmicsExpressionGenesExpectedCountProfile.csv file is incompatible with the PatientID in the Model file. As a result, there is no way to join the two...
View ArticleSelective dependencies
Is there a downloadable list of all selectively dependent genes called by both CRISPR and RNAi ? 1 post - 1 participant Read full topic
View ArticleDiscrepancy between Chronos InferredCommonEssentials and Web portal data
I have noticed that some genes which are considered common essential on the web portal (such as PPRC1 or ASH2L) are not found in the 23Q4 ChronosInferredCommonEssentials list. Is there a reason for...
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Repeated uniprot accesions and weird qvalues of proteomic data in the...
HI, I have some doubts about how the proteomic data is processed and how the qvalues are calculated on the custom analysis tool. Regarding the data, there are some gene symbols associated to multiple...
View ArticleCRISPR screens data for a drug effect
Hi, I am interested in results of the CRISPR screens that identify genes that modulate the response (protect or sensitize) to osimertinib in a sensitive cell line. How can I find these data? 1 post -...
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P-values and q-values are identical for custom analysis of drug sensitivity AUC?
I am using the custom analysis function to output Drug sensitivity AUC (Prism Repurposing Secondary Screen) correlations and q-values (See attached image). However, almost of the calculated p-values...
View ArticleDifferential analysis on gene expression data
Hi I am wondering if there is any pipeline for differential analysis on log2(TPM+1) data? Can I simplify use limma or other R package recommended? Thanks ahead for your comments. 1 post - 1...
View ArticleCell line susceptibility to lentiviral infection
Does the DepMap team have metadata on the susceptibility of different cell lines to lentiviral infection? It would be very useful to know how easy it is to infect different DepMap cell lines with...
View ArticleCell Viability of CRISPR dataset
I want to utilize cell viability data after CRISPR treatment. I guess ‘KYLogfoldChange’, ‘HumagneLogfoldChange’, ‘HumagneLogfoldChange’ data in 23Q4 are cell viability data. But, ‘README’ says...
View ArticleLength of assay for paralog screens
Hello, Are the growth conditions for the paralog screens recently released described anywhere? I am particularly interested in the length of the the assay. Thanks, Artur 1 post - 1 participant Read...
View ArticleOmicsCNGene.csv lacks some of the key oncogene data
Hi, I am trying to analyze the OmicsCNGene.csv file to get the copy number gains and loss information for some of the key oncogenes we are interested in (like MYC, CDKN2A etc.). These gene...
View Articlecell line selector list not available in scatter plot
I have generated lists using cell line selector, but the new lists are not displaying as an option to highlight on the scatterplot. I can still select my old lists, and when I look in the cell line...
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