Dear Kristian, This is very important question. Thanks for checking in. The manuscript is under review, and I believe that we already agreed and followed to Depmap’s policies. The input data we used in this package here contains only a subset of the data we used in the manuscript, and it is for demonstration how the package works. In addition to this, Deeptarget does have a function to pull out the data from Depmap and it is called Depmap2DeepTarget. I think this is where your concern is coming from. This function we incorporated the Depmap package from @Laurent Gatto<mailto:laurent.ga...@uclouvain.be> which allows users to download data from depmap.org. Therefore, I would love to leave this for @Laurent Gatto<mailto:laurent.ga...@uclouvain.be> to chime in to address your concern.
Thanks, Trinh From: Kristian Ullrich <ullr...@evolbio.mpg.de> Date: Wednesday, June 12, 2024 at 2:42 AM To: Nguyen, Trinh (NIH/NCI) [C] <tinh.ngu...@nih.gov> Cc: Kern, Lori <lori.sheph...@roswellpark.org>, bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [EXTERNAL] Re: [Bioc-devel] Deeptarget package Dear Nguyen, I have a question related to the data that you use and I just bring it up here since I would also like to ask the bioconductor developers, how this can be handled properly. The depmap.org<http://depmap.org/> portal has a clear "Terms and Condition" statement that you need to agree on if one uses any of the data that is provided by the portal. (See below) So one need to click a "I agree" button to stick to their policies. How have you managed that a user of your package first send this agreement to the depmap.org<http://depmap.org/> portal once the user uses data from the portal? Thank you in anticipation Best regards Kristian Here is their policy: " Terms and Conditions By using this site, you agree to our terms and conditions below. Overview of Terms These Terms of Use reflect the Broad Institute’s commitment to Open Science through its mission to provide freely available online services, databases and software relating to data contributed from life science experiments to the largest possible community. They impose no additional constraints on the use of the contributed data than those provided by the original data owners. The data made available on this website were generated for research purposes and are not intended for clinical use. The original data may be subject to rights claimed by third parties, including but not limited to, patent, copyright, other intellectual property rights, biodiversity-related access and benefit-sharing rights. 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Privacy See our privacy policy here<https://depmap.org/portal/privacy/>. " -- Kristian Ullrich, Ph.D. Max Planck Institute For Evolutionary Biology Scientific IT group Department of Evolutionary Genetics August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullr...@evolbio.mpg.de<mailto:ullr...@evolbio.mpg.de> “Ich weiß, allen tut's leid. Jeder muss gucken, wo er bleibt. Dein Lohn, so gut wie nichts. Nichts, was du tust, fällt ins Gewicht.” (Die traurigen Hummer; Moritz Krämer) -- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. On 11. Jun 2024, at 20:04, Nguyen, Trinh (NIH/NCI) [C] via Bioc-devel <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> wrote: Thank You! Trinh From: Kern, Lori <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>> Date: Tuesday, June 11, 2024 at 12:19 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>, Nguyen, Trinh (NIH/NCI) [C] <tinh.ngu...@nih.gov<mailto:tinh.ngu...@nih.gov>> Subject: [EXTERNAL] Re: Deeptarget package Two things: 1. The package was accepted on Friday. Currently our software builds are only building twice a week Tue and Fri. You can see the schedule of all the different builds at https://bioconductor.org/checkResults/. Eventually devel Bioc will go back to daily builds but there are some configurations we are currently working on. Once the package builds/checks cleanly on the daily builder it will then be available (likely later today) 1. Your package will only be available in Bioc devel 3.19 until the fall release as newly accepted package are placed until devel until a full release announcement. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of Nguyen, Trinh (NIH/NCI) [C] via Bioc-devel <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Sent: Tuesday, June 11, 2024 12:10 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subject: [Bioc-devel] Deeptarget package Dear Bioconductor team, Deeptarget package has been accepted. However, when I installed it has error of �package �DeepTarget� is not available for Bioconductor version '3.18'� Could you please give me some guidance? 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