# \#documentation **URL:** https://forum.depmap.org/tag/documentation/6.md [Latest](https://forum.depmap.org/latest.md) · [Categories](https://forum.depmap.org/categories.md) · [Tags](https://forum.depmap.org/tags.md) --- ## [Has Chronos2 been adopted in DepMap 25Q3 for gene-effect estimation?](https://forum.depmap.org/t/has-chronos2-been-adopted-in-depmap-25q3-for-gene-effect-estimation/4539)
**Author:** [@Jeffrey25](https://forum.depmap.org/u/Jeffrey25)\ **Replies:** 1\ **Last updated:** [January 6, 2026, 8:59pm UTC](https://forum.depmap.org/t/has-chronos2-been-adopted-in-depmap-25q3-for-gene-effect-estimation/4539 "2026-01-06T20:59:53Z")
Hi DepMap team, I have a question regarding the model used for gene-effect estimation in the most recent releases. I’m aware that Chronos was introduced starting in DepMap 21Q3. Recently, a new version — Chronos2 — wa… --- ## [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… --- ## [Details of CRISPR experiment: ScreenSequenceMap.csv](https://forum.depmap.org/t/details-of-crispr-experiment-screensequencemap-csv/4021)
**Author:** [@Mr\_Epimetheus](https://forum.depmap.org/u/Mr_Epimetheus)\ **Replies:** 1\ **Last updated:** [March 7, 2025, 4:15pm UTC](https://forum.depmap.org/t/details-of-crispr-experiment-screensequencemap-csv/4021 "2025-03-07T16:15:08Z")
Hello, I would like to know the specific process of conducting CRISPR experiments on DepMap However, I couldn’t find the ScreenSequenceMap.csv mentioned on the webpage. I also tried other search methods but still c… --- ## [Copy\_Number\_(Absolute) and OmicsAbsoluteCNGene are Different](https://forum.depmap.org/t/copy-number-absolute-and-omicsabsolutecngene-are-different/3677)
**Author:** [@Mr\_Epimetheus](https://forum.depmap.org/u/Mr_Epimetheus)\ **Replies:** 1\ **Last updated:** [October 24, 2024, 6:09pm UTC](https://forum.depmap.org/t/copy-number-absolute-and-omicsabsolutecngene-are-different/3677 "2024-10-24T18:09:02Z")
Hello, I have noticed that there is a significant difference between the Copy\_Number\_(Absolute) data in the Custom Downloads interface and the OmicsAbsoluteCNGene data in the All Data interface, both in terms of the numb… --- ## [Total number of cancer dependency genes / proteins across all cancer cell lines](https://forum.depmap.org/t/total-number-of-cancer-dependency-genes-proteins-across-all-cancer-cell-lines/3211)
**Author:** [@Marty\_A](https://forum.depmap.org/u/Marty_A)\ **Replies:** 1\ **Last updated:** [April 26, 2024, 3:58pm UTC](https://forum.depmap.org/t/total-number-of-cancer-dependency-genes-proteins-across-all-cancer-cell-lines/3211 "2024-04-26T15:58:20Z")
Hi, is there any easy way to find the total number of cancer dependency genes / proteins across all cancer cell lines or a rough approximation as of 2024? --- ## [Definition of common essential genes](https://forum.depmap.org/t/definition-of-common-essential-genes/3171)
**Author:** [@Allan\_Lui](https://forum.depmap.org/u/Allan_Lui)\ **Replies:** 0\ **Last updated:** [April 2, 2024, 1:00am UTC](https://forum.depmap.org/t/definition-of-common-essential-genes/3171 "2024-04-02T01:00:51Z")
In the web portal, common essential genes are defined as: A gene which, in a large, pan-cancer screen, ranks in the top X most depleting genes in at least 90% of cell lines. X is chosen empirically using the minimum of t… --- ## [Cell Line Molecular Subtypes](https://forum.depmap.org/t/cell-line-molecular-subtypes/2941)
**Author:** [@ag89](https://forum.depmap.org/u/ag89)\ **Replies:** 0\ **Last updated:** [November 29, 2023, 6:13pm UTC](https://forum.depmap.org/t/cell-line-molecular-subtypes/2941 "2023-11-29T18:13:37Z")
Hi, I’m looking for a file that has all cell lines listed along with their molecular subtypes. I know in 23Q2, Model.csv has some listed under LegacyMolecularSubtype, but I’m wondering if there’s anyplace this is better… --- ## [OncotreeCode CMLBCRABL1 does not include all cell lines with BCR-ABL fusion](https://forum.depmap.org/t/oncotreecode-cmlbcrabl1-does-not-include-all-cell-lines-with-bcr-abl-fusion/2727)
**Author:** [@bkinedi](https://forum.depmap.org/u/bkinedi)\ **Replies:** 2\ **Last updated:** [August 3, 2023, 10:02am UTC](https://forum.depmap.org/t/oncotreecode-cmlbcrabl1-does-not-include-all-cell-lines-with-bcr-abl-fusion/2727 "2023-08-03T10:02:06Z")
Hi, I’ve been working with lymphoid and myeloid cell lines recently and noticed that the majority of CML cell lines are referenced by their OncotreeCode of CML, whilst a few others are referenced by CMLBCRABL1. I had a … --- ## [Difference between Mifepristone Compounds](https://forum.depmap.org/t/difference-between-mifepristone-compounds/2726)
**Author:** [@DanielG](https://forum.depmap.org/u/DanielG)\ **Replies:** 0\ **Last updated:** [July 28, 2023, 3:58pm UTC](https://forum.depmap.org/t/difference-between-mifepristone-compounds/2726 "2023-07-28T15:58:24Z")
Hi, My group and I performed a primary drug screen two-class comparison to investigate how a particular mutation in our cancer type predicts for drug sensitivity or resistance based on a particular drug’s mechanism of a… --- ## [A question about the naming of cell lines](https://forum.depmap.org/t/a-question-about-the-naming-of-cell-lines/2622)
**Author:** [@fangli](https://forum.depmap.org/u/fangli)\ **Replies:** 2\ **Last updated:** [June 14, 2023, 1:37pm UTC](https://forum.depmap.org/t/a-question-about-the-naming-of-cell-lines/2622 "2023-06-14T13:37:29Z")
Hello, I have a question about the OmicsExpressionGenesExpectedCountProfile.csv file. I noticed that the cell lines in this file are named with PR- prefix, not the ACH- prefix that I usually see. How can I map the PR- pr… --- ## [DepMap Protein Array (RPPA) Data](https://forum.depmap.org/t/depmap-protein-array-rppa-data/2230)
**Author:** [@dujudy](https://forum.depmap.org/u/dujudy)\ **Replies:** 0\ **Last updated:** [January 25, 2023, 2:21pm UTC](https://forum.depmap.org/t/depmap-protein-array-rppa-data/2230 "2023-01-25T14:21:16Z")
How is Validation\_Status determined? How is a “Validated” status discerned from “Caution”? --- ## [How to inverse the AUC value for drug sensitivity screens](https://forum.depmap.org/t/how-to-inverse-the-auc-value-for-drug-sensitivity-screens/2175)
**Author:** [@LJMH](https://forum.depmap.org/u/LJMH)\ **Replies:** 0\ **Last updated:** [January 5, 2023, 2:31pm UTC](https://forum.depmap.org/t/how-to-inverse-the-auc-value-for-drug-sensitivity-screens/2175 "2023-01-05T14:31:20Z")
I am using the CTRP2 dataset and I’m interested to use AUC as a measure of drug sensitivity. For the analysis I want to run, the interpretation would be simplified if could inverse this value, that is, the area above the… --- ## [Depmap CSV files](https://forum.depmap.org/t/depmap-csv-files/1326)
**Author:** [@abalter](https://forum.depmap.org/u/abalter)\ **Replies:** 3\ **Last updated:** [April 27, 2022, 5:41pm UTC](https://forum.depmap.org/t/depmap-csv-files/1326 "2022-04-27T17:41:12Z")
There are hella files at the download page Is there a data dictionary and/or schema for these files? I realize that there is probably information in papers, but it is also true that the data and formats are updated wh… --- ## [Finding data licenses](https://forum.depmap.org/t/finding-data-licenses/1243)
**Author:** [@dzerbino](https://forum.depmap.org/u/dzerbino)\ **Replies:** 2\ **Last updated:** [March 29, 2022, 4:42pm UTC](https://forum.depmap.org/t/finding-data-licenses/1243 "2022-03-29T16:42:16Z")
Hello, What is the best way to determine the data license governing the usage of a file available for download on the DepMap portal? Thank you, Daniel --- ## [What is relative copy number/copy number ratio?](https://forum.depmap.org/t/what-is-relative-copy-number-copy-number-ratio/104)
**Author:** [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\ **Replies:** 13\ **Last updated:** [February 9, 2022, 10:18pm UTC](https://forum.depmap.org/t/what-is-relative-copy-number-copy-number-ratio/104 "2022-02-09T22:18:40Z")
Users have asked us: What is relative copy number/copy number ratio? --- ## [Are 21Q4 CCLE\_wes\_gene\_cn.csv copy number data log2-transformed](https://forum.depmap.org/t/are-21q4-ccle-wes-gene-cn-csv-copy-number-data-log2-transformed/1165)
**Author:** [@ming](https://forum.depmap.org/u/ming)\ **Replies:** 1\ **Last updated:** [January 31, 2022, 8:13pm UTC](https://forum.depmap.org/t/are-21q4-ccle-wes-gene-cn-csv-copy-number-data-log2-transformed/1165 "2022-01-31T20:13:00Z")
For version 21Q4, there are two more files: CCLE\_wes\_gene\_cn.csv and CCLE\_wes\_segment\_cn.csv. From the README file, the CCLE\_wes\_gene\_cn.csv described the gene level copy number data and log2-transformed with a pseudo co… --- ## [Estimation of uncertainty around the dose-response curve](https://forum.depmap.org/t/estimation-of-uncertainty-around-the-dose-response-curve/243)
**Author:** [@kara](https://forum.depmap.org/u/kara)\ **Replies:** 1\ **Last updated:** [January 11, 2022, 3:57pm UTC](https://forum.depmap.org/t/estimation-of-uncertainty-around-the-dose-response-curve/243 "2022-01-11T15:57:16Z")
Hi everyone, I was wondering, how do you estimate the uncertainty around the AUC value for the drug screens? Some of the cell lines were tested in 2-3 replicates and some in 6, that would influence how certain we are o… --- ## [Compound annotations/translating BRD ID's](https://forum.depmap.org/t/compound-annotations-translating-brd-ids/953)
**Author:** [@Pascal](https://forum.depmap.org/u/Pascal)\ **Replies:** 1\ **Last updated:** [October 21, 2021, 7:28pm UTC](https://forum.depmap.org/t/compound-annotations-translating-brd-ids/953 "2021-10-21T19:28:47Z")
Hey there, I am using the drug sensitivity data for modeling. I need to identify the compounds. Where do I find the drug annotations? How do I translate from a BRD ID to, for example, INCHI key? Thanks! Best Regards P… --- ## [miRNA Metadata Update](https://forum.depmap.org/t/mirna-metadata-update/807)
**Author:** [@Erin\_Piazza](https://forum.depmap.org/u/Erin_Piazza)\ **Replies:** 4\ **Last updated:** [October 16, 2021, 12:34am UTC](https://forum.depmap.org/t/mirna-metadata-update/807 "2021-10-16T00:34:40Z")
Hi DepMap Team! I am on the bioinformatics team at NanoString and received an inquiry regarding the miRNA data for CCLE a few months ago. I contacted the old Broad site while they were transitioning to DepMap, so I’m ch… --- ## [Cell STRAINER documentation](https://forum.depmap.org/t/cell-strainer-documentation/893)
**Author:** [@blas](https://forum.depmap.org/u/blas)\ **Replies:** 1\ **Last updated:** [September 16, 2021, 1:32pm UTC](https://forum.depmap.org/t/cell-strainer-documentation/893 "2021-09-16T13:32:12Z")
Hello, I know Cell STRAINER tool uses Pearson’s R correlation between the uploaded copy-number values and those of the mathched CCLE line, but I can’t find documentation on how this calculation is performed. Do you know… --- ## [Cell line - SS1A](https://forum.depmap.org/t/cell-line-ss1a/826)
**Author:** [@Faberan](https://forum.depmap.org/u/Faberan)\ **Replies:** 1\ **Last updated:** [August 16, 2021, 2:44pm UTC](https://forum.depmap.org/t/cell-line-ss1a/826 "2021-08-16T14:44:08Z")
Could someone help with the cell line “SS1A” , It is listed as sarcoma without a subset, it has synovial sarcoma dependencies (SS18, etc) and, of course, it is named SS1A. Yet it not categorized as synovial. I cannot fin… --- ## [Mutation frequency](https://forum.depmap.org/t/mutation-frequency/680)
**Author:** [@rojinsafavi](https://forum.depmap.org/u/rojinsafavi)\ **Replies:** 1\ **Last updated:** [June 28, 2021, 2:43pm UTC](https://forum.depmap.org/t/mutation-frequency/680 "2021-06-28T14:43:18Z")
Could you please clarify which column corresponds to mutation frequency? --- ## [Definitions of the 21Q2 mutations 'damaging', 'nonconserving', 'otherconserving' files](https://forum.depmap.org/t/definitions-of-the-21q2-mutations-damaging-nonconserving-otherconserving-files/621)
**Author:** [@Shawn](https://forum.depmap.org/u/Shawn)\ **Replies:** 1\ **Last updated:** [May 26, 2021, 3:14pm UTC](https://forum.depmap.org/t/definitions-of-the-21q2-mutations-damaging-nonconserving-otherconserving-files/621 "2021-05-26T15:14:49Z")
Hi, I was wondering if we could get a definition of how the boolean matrices were created? I’m assuming ‘bool\_hotspot’ is 1 if the TCGA or COMSIC HotSpot column is true. However, for the ‘damaging’ file, how are you de… --- ## [Missing data field in 20Q4 v2 segment level copy number data](https://forum.depmap.org/t/missing-data-field-in-20q4-v2-segment-level-copy-number-data/426)
**Author:** [@brodriguez](https://forum.depmap.org/u/brodriguez)\ **Replies:** 2\ **Last updated:** [February 1, 2021, 6:13pm UTC](https://forum.depmap.org/t/missing-data-field-in-20q4-v2-segment-level-copy-number-data/426 "2021-02-01T18:13:10Z")
The 20Q4 v2 CCLE\_segment\_cn.csv file description lists a seventh column, ‘amplification status (+,-,0)’ which is not present in the file. Regards, Ben --- ## [Common essential genes](https://forum.depmap.org/t/common-essential-genes/277)
**Author:** [@ASWANI\_KRISHNA](https://forum.depmap.org/u/ASWANI_KRISHNA)\ **Replies:** 3\ **Last updated:** [January 16, 2021, 5:15pm UTC](https://forum.depmap.org/t/common-essential-genes/277 "2021-01-16T17:15:24Z")
What will be the effect of common essential genes in normal cells? Are they only essential for cancer cell lines? --- ## [How to use the DepMap data to define negative genetic interactions?](https://forum.depmap.org/t/how-to-use-the-depmap-data-to-define-negative-genetic-interactions/305)
**Author:** [@yahui\_long](https://forum.depmap.org/u/yahui_long)\ **Replies:** 1\ **Last updated:** [December 8, 2020, 3:13pm UTC](https://forum.depmap.org/t/how-to-use-the-depmap-data-to-define-negative-genetic-interactions/305 "2020-12-08T15:13:13Z")
Hello. I have two questions. The first question is that how to define the interaction score of two genes according to CRISPR (Avana) Public 20Q4? Any suggestions? The second question is that what do the Pearson correlat… --- ## [Retired DepMap IDs](https://forum.depmap.org/t/retired-depmap-ids/231)
**Author:** [@coryandar](https://forum.depmap.org/u/coryandar)\ **Replies:** 1\ **Last updated:** [October 8, 2020, 3:58pm UTC](https://forum.depmap.org/t/retired-depmap-ids/231 "2020-10-08T15:58:34Z")
I’ve noticed there’s a fair amount of depmap ids that seem to be retired. Is there an official, running list of these ids? Trying to ensure my future analysis can be integrated with older work. Example: The depmap id: … --- ## [Cell line data download](https://forum.depmap.org/t/cell-line-data-download/196)
**Author:** [@maryam\_shakeri](https://forum.depmap.org/u/maryam_shakeri)\ **Replies:** 1\ **Last updated:** [September 16, 2020, 8:37pm UTC](https://forum.depmap.org/t/cell-line-data-download/196 "2020-09-16T20:37:39Z")
Hi I’ve been using data from the expression public 20q2 set, where there is one measurement of gene expression for each cell line. I am interested in comparing gene expression levels to each other, across different cell …