Multiple SMILES in secondary-screen-dose-response-curve-parameters.csv
Hello, I hope this message finds you well. I am currently working with the dataset in the file secondary-screen-dose-response-curve-parameters.csv and noticed that the “smiles” column contains...
View ArticleAvailability of of RNA-seq bigwig files
Hello, I am looking for RNA-seq genome-wide coverage data in bigwig format (instead of table with expression per gene). Is this level of data available? Or a level of data that could be converted to...
View ArticleNormalization -TMM
Hi I want to understand that if I have to do TMM normalization rather than using TPM as TPM is not considered a very good parameter to compare across different samples. Which file with Raw reads would...
View ArticleNegative goodness of fit
Dear DepMap team, Why some r2 values in the Prism secondary-screen-dose-response-curve-parameters.csv file are negative? Isn’t r2 bounded between 0 and 1? Thanks 1 post - 1 participant Read full topic
View ArticleNon-breaking space in Model.csv current version (2024Q4)
Hi - Minor but I hit a potential problem using the current (2024Q4) version of Model.csv. For the entry for model ID ACH-000938, for the field ModelSubtypeFeatures, it contains “DUX4” and then some...
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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 ArticleStranded profiles in unstranded expected counts csv
(topic deleted by author) 1 post - 1 participant Read full topic
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...
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