# Q&A **URL:** https://forum.depmap.org/c/qa/5.md?page=2 [Latest](https://forum.depmap.org/latest.md) · [Categories](https://forum.depmap.org/categories.md) · [Tags](https://forum.depmap.org/tags.md) **Page:** 3 --- ## [Predicted CRISPR KO gene score (precursor to Predictability score)](https://forum.depmap.org/t/predicted-crispr-ko-gene-score-precursor-to-predictability-score/4423)
**Author:** [@HoangDinh](https://forum.depmap.org/u/HoangDinh)\ **Replies:** 2\ **Last updated:** [August 19, 2025, 3:25pm UTC](https://forum.depmap.org/t/predicted-crispr-ko-gene-score-precursor-to-predictability-score/4423 "2025-08-19T15:25:42Z")
Hello. I am thinking that to generate the Predictability score the Machine Learning (ML) models first generate the gene knockout scores so that pearson correlation can be calculated. Is this correct? If so, I am interes… --- ## [Availability of DepMap 25Q2 On FigShare](https://forum.depmap.org/t/availability-of-depmap-25q2-on-figshare/4424)
**Author:** [@Matthew\_Crown](https://forum.depmap.org/u/Matthew_Crown)\ **Replies:** 1\ **Last updated:** [August 18, 2025, 12:50pm UTC](https://forum.depmap.org/t/availability-of-depmap-25q2-on-figshare/4424 "2025-08-18T12:50:23Z")
Hi, I noticed that DepMap 25Q2 has not had an associated FigShare release and that the files are now downloaded from AWS on the site. Are there any plans to make the release available on FigShare? --- ## [Model level data for other omics (RPPA, Mass Spec and Methylation data)](https://forum.depmap.org/t/model-level-data-for-other-omics-rppa-mass-spec-and-methylation-data/4397)
**Author:** [@jkreis](https://forum.depmap.org/u/jkreis)\ **Replies:** 1\ **Last updated:** [August 8, 2025, 1:51pm UTC](https://forum.depmap.org/t/model-level-data-for-other-omics-rppa-mass-spec-and-methylation-data/4397 "2025-08-08T13:51:21Z")
Hello, Thanks a lot for this great resource. Currently the OmicsProfiles file only lists rna,wgs and wes data. How do I know which condition was used for other omics? thanks in advance! --- ## [Screening date metadata](https://forum.depmap.org/t/screening-date-metadata/4394)
**Author:** [@lough](https://forum.depmap.org/u/lough)\ **Replies:** 0\ **Last updated:** [August 5, 2025, 4:24pm UTC](https://forum.depmap.org/t/screening-date-metadata/4394 "2025-08-05T16:24:22Z")
Hi, Thanks for this resource. I’m working on a cancer evolution project aiming to analyse gene essentiality and drug sensitivity at certain genomic copy number states. However, as copy number states can evolve and disap… --- ## [GISTIC2 Analysis of cBioPortal Segment-Level CN Data](https://forum.depmap.org/t/gistic2-analysis-of-cbioportal-segment-level-cn-data/4391)
**Author:** [@Sharon\_Bader](https://forum.depmap.org/u/Sharon_Bader)\ **Replies:** 1\ **Last updated:** [August 5, 2025, 1:34pm UTC](https://forum.depmap.org/t/gistic2-analysis-of-cbioportal-segment-level-cn-data/4391 "2025-08-05T13:34:12Z")
Hello, I’ve been interested in running GISTIC2 on the segment-level copy number data available via cBioPortal. I assume this analysis may have been performed internally, and perhaps the results have even been deposited… --- ## [Is there a threshold in Drug Sensitivity AUC?](https://forum.depmap.org/t/is-there-a-threshold-in-drug-sensitivity-auc/3038)
**Author:** [@cht](https://forum.depmap.org/u/cht)\ **Replies:** 7\ **Last updated:** [July 31, 2025, 9:05pm UTC](https://forum.depmap.org/t/is-there-a-threshold-in-drug-sensitivity-auc/3038 "2025-07-31T21:05:32Z")
Is there a threshold in Drug Sensitivity AUC, below which it is considered that the drug has an impact on cell line proliferation? which threshold? Similarly, does a threshold also exist in the PRISM Repurposing Prim… --- ## [ comparison between raw counts and log TPM values ](https://forum.depmap.org/t/comparison-between-raw-counts-and-log-tpm-values/4339)
**Author:** [@Abed\_Kurdi](https://forum.depmap.org/u/Abed_Kurdi)\ **Replies:** 6\ **Last updated:** [July 29, 2025, 5:45am UTC](https://forum.depmap.org/t/comparison-between-raw-counts-and-log-tpm-values/4339 "2025-07-29T05:45:54Z")
Hello there, I downloaded first the log TPM values and plotted them for a specific gene and found that it is expressed. Then, I have to use another normalization method and downloaded the raw counts. Checking the raw co… --- ## [Antibiotic doses?](https://forum.depmap.org/t/antibiotic-doses/4326)
**Author:** [@vasilisgr](https://forum.depmap.org/u/vasilisgr)\ **Replies:** 1\ **Last updated:** [July 24, 2025, 4:54am UTC](https://forum.depmap.org/t/antibiotic-doses/4326 "2025-07-24T04:54:29Z")
Is there a listing of antibiotic dose used for selection for each of the cell lines in DepMap anywhere? --- ## [How to label the cells in DepMap 2.0](https://forum.depmap.org/t/how-to-label-the-cells-in-depmap-2-0/4354)
**Author:** [@kscrevatis](https://forum.depmap.org/u/kscrevatis)\ **Replies:** 2\ **Last updated:** [July 15, 2025, 4:30pm UTC](https://forum.depmap.org/t/how-to-label-the-cells-in-depmap-2-0/4354 "2025-07-15T16:30:45Z")
I have been using DepMap v 1.0 for analyses where I would like to label the cells from a list of defined cell line context. Does anyone know how I can do this labeling in V 2.0? There used to be a button for labeling cel… --- ## [Availability of VCF/WGS data for cell line demultiplexing ](https://forum.depmap.org/t/availability-of-vcf-wgs-data-for-cell-line-demultiplexing/4155)
**Author:** [@Luca\_Zanella](https://forum.depmap.org/u/Luca_Zanella)\ **Replies:** 4\ **Last updated:** [July 14, 2025, 1:35pm UTC](https://forum.depmap.org/t/availability-of-vcf-wgs-data-for-cell-line-demultiplexing/4155 "2025-07-14T13:35:38Z")
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 reference genome, and… --- ## [comparison between raw counts and log TPM values](https://forum.depmap.org/t/comparison-between-raw-counts-and-log-tpm-values/4340)
**Author:** [@Abed\_Kurdi](https://forum.depmap.org/u/Abed_Kurdi)\ **Replies:** 0\ **Last updated:** [July 10, 2025, 2:16pm UTC](https://forum.depmap.org/t/comparison-between-raw-counts-and-log-tpm-values/4340 "2025-07-10T14:16:09Z")
Hello there, I downloaded first the log TPM values and plotted them for a specific gene and found that it is expressed. Then, I have to use another normalization method and downloaded the raw counts. Checking the raw co… --- ## [Random forest code](https://forum.depmap.org/t/random-forest-code/4261)
**Author:** [@bav](https://forum.depmap.org/u/bav)\ **Replies:** 2\ **Last updated:** [July 1, 2025, 2:12pm UTC](https://forum.depmap.org/t/random-forest-code/4261 "2025-07-01T14:12:26Z")
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 readme (https://www.bio… --- ## [Drug-Target validation using CRISPR and PRISM repurposing dataset](https://forum.depmap.org/t/drug-target-validation-using-crispr-and-prism-repurposing-dataset/4268)
**Author:** [@Mohamed\_El\_Moussaoui](https://forum.depmap.org/u/Mohamed_El_Moussaoui)\ **Replies:** 6\ **Last updated:** [July 1, 2025, 9:01am UTC](https://forum.depmap.org/t/drug-target-validation-using-crispr-and-prism-repurposing-dataset/4268 "2025-07-01T09:01:01Z")
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 (effects). however, i am lo… --- ## [Access to unfiltered cell line VCF files?](https://forum.depmap.org/t/access-to-unfiltered-cell-line-vcf-files/4312)
**Author:** [@anushaggs](https://forum.depmap.org/u/anushaggs)\ **Replies:** 1\ **Last updated:** [June 30, 2025, 1:09pm UTC](https://forum.depmap.org/t/access-to-unfiltered-cell-line-vcf-files/4312 "2025-06-30T13:09:37Z")
How can we access the unfiltered VCF files for the cell lines containing both coding and non-coding variants? --- ## [How is 'Haematopoietic And Lymphoid' coming as enriched lineages but are absent in the lineage columns of the cell line data?](https://forum.depmap.org/t/how-is-haematopoietic-and-lymphoid-coming-as-enriched-lineages-but-are-absent-in-the-lineage-columns-of-the-cell-line-data/4230)
**Author:** [@adhya05](https://forum.depmap.org/u/adhya05)\ **Replies:** 1\ **Last updated:** [June 26, 2025, 2:17pm UTC](https://forum.depmap.org/t/how-is-haematopoietic-and-lymphoid-coming-as-enriched-lineages-but-are-absent-in-the-lineage-columns-of-the-cell-line-data/4230 "2025-06-26T14:17:41Z")
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 columns ‘OncotreeL… --- ## [How to compare essential genes in several cell lines of certain lineage at once?](https://forum.depmap.org/t/how-to-compare-essential-genes-in-several-cell-lines-of-certain-lineage-at-once/4290)
**Author:** [@Idan](https://forum.depmap.org/u/Idan)\ **Replies:** 1\ **Last updated:** [June 26, 2025, 1:44pm UTC](https://forum.depmap.org/t/how-to-compare-essential-genes-in-several-cell-lines-of-certain-lineage-at-once/4290 "2025-06-26T13:44:53Z")
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 looking for essential gene… --- ## [Question about the naming rule for drugs in Custom Downloads data](https://forum.depmap.org/t/question-about-the-naming-rule-for-drugs-in-custom-downloads-data/4299)
**Author:** [@WYB](https://forum.depmap.org/u/WYB)\ **Replies:** 1\ **Last updated:** [June 26, 2025, 1:29pm UTC](https://forum.depmap.org/t/question-about-the-naming-rule-for-drugs-in-custom-downloads-data/4299 "2025-06-26T13:29:26Z")
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 if the names of dr… --- ## [WGS data access](https://forum.depmap.org/t/wgs-data-access/4300)
**Author:** [@SKE](https://forum.depmap.org/u/SKE)\ **Replies:** 1\ **Last updated:** [June 23, 2025, 1:00pm UTC](https://forum.depmap.org/t/wgs-data-access/4300 "2025-06-23T13:00:47Z")
Hi, Is it possible to access WGS data (FASTQ or BAM files) for specific cell lines from the database? Thanks in advance! --- ## [Cell line annotations](https://forum.depmap.org/t/cell-line-annotations/3900)
**Author:** [@hjt](https://forum.depmap.org/u/hjt)\ **Replies:** 2\ **Last updated:** [June 16, 2025, 1:05pm UTC](https://forum.depmap.org/t/cell-line-annotations/3900 "2025-06-16T13:05:49Z")
hello,I would like to know if the DepMap 24Q4 data includes files with detailed annotations for cell lines,thank you for your help --- ## [BAM files from RNA seq](https://forum.depmap.org/t/bam-files-from-rna-seq/4282)
**Author:** [@jtl](https://forum.depmap.org/u/jtl)\ **Replies:** 1\ **Last updated:** [June 13, 2025, 5:38pm UTC](https://forum.depmap.org/t/bam-files-from-rna-seq/4282 "2025-06-13T17:38:06Z")
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 elswhere. Thanks in ad… --- ## [Cannot share reports](https://forum.depmap.org/t/cannot-share-reports/4267)
**Author:** [@kdvnfphmlp](https://forum.depmap.org/u/kdvnfphmlp)\ **Replies:** 1\ **Last updated:** [June 9, 2025, 12:58pm UTC](https://forum.depmap.org/t/cannot-share-reports/4267 "2025-06-09T12:58:47Z")
When I click share button in the reports, its not responding. I’m using Chrome and even when I use Edge the bug remains --- ## [Data after CRISPR-Cas9 screening](https://forum.depmap.org/t/data-after-crispr-cas9-screening/4252)
**Author:** [@SongSong](https://forum.depmap.org/u/SongSong)\ **Replies:** 2\ **Last updated:** [June 9, 2025, 2:34am UTC](https://forum.depmap.org/t/data-after-crispr-cas9-screening/4252 "2025-06-09T02:34:30Z")
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 screening? Although there… --- ## [DepMap Data – Exploring Relevance Beyond Oncology](https://forum.depmap.org/t/depmap-data-exploring-relevance-beyond-oncology/4251)
**Author:** [@clearfork01](https://forum.depmap.org/u/clearfork01)\ **Replies:** 0\ **Last updated:** [June 2, 2025, 7:40pm UTC](https://forum.depmap.org/t/depmap-data-exploring-relevance-beyond-oncology/4251 "2025-06-02T19:40:01Z")
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 oncology and cancer geno… --- ## [Some files cannot be downloaded!](https://forum.depmap.org/t/some-files-cannot-be-downloaded/4229)
**Author:** [@Deptective](https://forum.depmap.org/u/Deptective)\ **Replies:** 0\ **Last updated:** [May 26, 2025, 4:48pm UTC](https://forum.depmap.org/t/some-files-cannot-be-downloaded/4229 "2025-05-26T16:48:52Z")
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 points to: https:/… --- ## [NCI-H854 Oncotree cancer type](https://forum.depmap.org/t/nci-h854-oncotree-cancer-type/4189)
**Author:** [@wshao](https://forum.depmap.org/u/wshao)\ **Replies:** 1\ **Last updated:** [May 23, 2025, 4:32pm UTC](https://forum.depmap.org/t/nci-h854-oncotree-cancer-type/4189 "2025-05-23T16:32:09Z")
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 tumor, but the SampleC… --- ## [Data "PRISM Repurposing Public 24Q2" in Custom Downloads](https://forum.depmap.org/t/data-prism-repurposing-public-24q2-in-custom-downloads/4219)
**Author:** [@WYB](https://forum.depmap.org/u/WYB)\ **Replies:** 1\ **Last updated:** [May 23, 2025, 3:31pm UTC](https://forum.depmap.org/t/data-prism-repurposing-public-24q2-in-custom-downloads/4219 "2025-05-23T15:31:01Z")
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 the acquisition of the… --- ## [How to Best Analyze DepMap Data for Identifying Cancer Dependencies?](https://forum.depmap.org/t/how-to-best-analyze-depmap-data-for-identifying-cancer-dependencies/4228)
**Author:** [@Sakura](https://forum.depmap.org/u/Sakura)\ **Replies:** 0\ **Last updated:** [May 23, 2025, 2:24pm UTC](https://forum.depmap.org/t/how-to-best-analyze-depmap-data-for-identifying-cancer-dependencies/4228 "2025-05-23T14:24:17Z")
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 analysis. I want to identi… --- ## [How do we interpret the ssGSEA scores in DepMap?](https://forum.depmap.org/t/how-do-we-interpret-the-ssgsea-scores-in-depmap/4218)
**Author:** [@kscrevatis](https://forum.depmap.org/u/kscrevatis)\ **Replies:** 1\ **Last updated:** [May 23, 2025, 1:34pm UTC](https://forum.depmap.org/t/how-do-we-interpret-the-ssgsea-scores-in-depmap/4218 "2025-05-23T13:34:12Z")
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 represents a gene signature … --- ## [Prism compound and cell line count](https://forum.depmap.org/t/prism-compound-and-cell-line-count/4201)
**Author:** [@selina](https://forum.depmap.org/u/selina)\ **Replies:** 0\ **Last updated:** [May 10, 2025, 7:02pm UTC](https://forum.depmap.org/t/prism-compound-and-cell-line-count/4201 "2025-05-10T19:02:03Z")
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 many compounds have b… --- ## [DepMap portal cell line mutation,](https://forum.depmap.org/t/depmap-portal-cell-line-mutation/4186)
**Author:** [@dizysky](https://forum.depmap.org/u/dizysky)\ **Replies:** 2\ **Last updated:** [May 5, 2025, 3:00pm UTC](https://forum.depmap.org/t/depmap-portal-cell-line-mutation/4186 "2025-05-05T15:00:33Z")
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 (broad 2019 data, … [Previous page](https://forum.depmap.org/c/qa/5.md?page=1) [Next page](https://forum.depmap.org/c/qa/5.md?page=3)