Batch_corrected_Expression_Public_24Q2
I have downloaded Batch_corrected_Expression_Public_24Q2 data. I understood that they have integrated Project Achilis and Score’s dataset. But, how ? What is the total preprocessing and data cleaning...
View Articlewhat file is suitable for differential expression analysis
hi, I would like to perform differential expression analysis between cell line. for that I need raw count expression data. I wonder what file is suitable for this matter as I saw several different...
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Comparison between two cell lines
Hello, I’m trying to compare gene expression of two cell lines but an error occurs This doesn’t happen with groups with more than two cell lines 1 post - 1 participant Read full topic
View Article24Q4 Data - timeline?
Hi, I was wondering if we are still on track to have the 24Q4 data uploaded in November? Hoping to start some work and would prefer latest datasets if it’ll be available before the end of the month....
View Articlesample ID not match in 'OmicsFusionFiltered' and 'OmicsFusionUnfilteredProfile'
Hi, Could you provide matched sample ID in these two files? These files use different sample ID. OmicsFusionFiltered shows the ModelID, but OmicsFusionUnfilteredProfile file shows the ProfileID. I...
View ArticleWGS data
Hi I see the WGS data from ENA Browser. It says there are 329 cell lines’ WGS data. But, from Data | DepMap Portal, I see 559 cell lines’ WGS data. I wonder where and when I can download the rest of...
View ArticleCell viability data
Hello, I would like to know how can I retrieve the cell viability data based on RNAi or CRISPR in human lung cancer cell lines? What does ‘Effect Size Means Difference’ mean in the dependencies...
View ArticleWhat's the genome version and gene annotation file used for Depmap bulk...
Dear Sir./Madam., Can I know what’s the genome version and gene annotation file (e.g. Gencode or Ensembl, which version) used for Depmap bulk RNA-Seq expression estimation? Thanks, Bo 2 posts - 2...
View ArticleNon-Cancerous and Primary or Metastatic cell lines
Hi, How come some of Non-Cancerous cases have Primary or Metastatic labels? Best, Saed OncotreePrimary Disease PrimaryOrMetastasis Count Non-Cancerous Metastatic 4 Non-Cancerous Primary 15...
View Articlecell line id
I have a question. I have a cell line number in each row of this table that is not a depmap ID. However, I need to convert these cell lines to depmap IDs in batches, otherwise my work will be...
View ArticleChronos score
I would like to know if a gene effect Chronos score greater than 0 indicates that the growth rate of the cell line will increase after the gene is knocked out. I have noticed that there are many genes...
View ArticleWhy isn't all of the cell line annotation data in one place?
The model.csv table contains important annotations such as breast cancer ER, PR and HER2 status which does not seem to be in context manager. However the context manager has information such as...
View ArticleAbsolute copy number
The current data version has been upgraded to 24Q2, and there is also Gene-level absolute copy number data (OmicsAbsoluteCNGene.csv). Why is the copy number data displayed on the interface still from...
View ArticleIGHG1 missing data or bad reference to data?
When navigating to the Overview tab of IGHG1, the following message is displayed: Sorry, an error occurred. https://depmap.org/portal/gene/IGHG1?tab=overview 2 posts - 2 participants Read full topic
View ArticleDepMap Metadata
The DepMap Portal’s metadata files provides essential contextual information about data available on the platform and allows researchers to understand the context and limitations of the data,...
View ArticleDepMap Portal Datasets
The DepMap project continuously generates new data and tools as well as integrates existing data into the DepMap framework. All datasets either generated or integrated by DepMap are available to use...
View ArticleHow can I obtain DepMap cell lines?
DepMap commonly provides the sources of cell lines used for data generation found on the portal. Cell lines may either be purchased through commercial vendors or be donated by academic labs across the...
View ArticleHow should I site DepMap data?
Data in the DepMap portal is available for the community to use. The DepMap team does not need to be included as authors should you seek to publish on the data, but we do ask that you use the...
View ArticleDepMap Overview
The Cancer Dependency Map (DepMap) is committed to systematically accelerating precision cancer medicine by developing comprehensive, large-scale functional datasets that are publicly accessible to...
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Repurposing Datasets (2019 - 2023)
The PRISM Repurposing dataset contains small molecule viability data generated using the Broad Repurposing Library and the PRISM multiplexed cell-line viability assay. This public resource contains...
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