The maintainer for these two packages IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Is actually Kasper Daniel Hansen as listed in the DESCRIPTION file not bioc core members. You could reach out to Kasper to see if there is any intention or efforts that have already been made to include v2. If not you can submit the packages. We have moved away from traditional annotation packages and I would suggest moving towards an annotationhub package submission where the data is stored elsewhere on a external server like S3 buckets, Azure Data Lakes, Zenodo, etc.... (we have an bioconductor azure data lake location that can be used; it just cannot be store on any personal location like github or dropbox) Little modification to an existing package structure is needed. Basically you would remove the data to the external location, include a metadata.csv file in the inst/extdata, and include the biocView AnnotationHub. More details can be found at https://bioconductor.org/packages/release/bioc/vignettes/HubPub/inst/doc/CreateAHubPackage.html Then submit as normal to the new package submission tracker. Cheers, 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> on behalf of Zuguang Gu <joker...@gmail.com> Sent: Saturday, March 18, 2023 3:56 PM To: bioc-devel <bioc-devel@r-project.org> Subject: [Bioc-devel] Manifest and annotation packages for EPIC methylation array v2.0 Hi Bioc-devel, I recently analyzed a methylation array dataset which is from EPIC array v2.0 ( https://secure-web.cisco.com/1lqTYM1ya8XGMtHfnsdUpS8GBFfG2-c035Su1G2QlTqVVUgHKjstjf7gJtWM-rIZGvRTc76YuWsBkkII9eMBecVmP2e1A55mf2ahOVb9Nco1iHMg44efGw-SU_hREgUNlB7o5Sy6C-OATItf9L-NsoDSZnhzqs8WSnCWLDCRBlqDX8bOOoHRQ-xf-Ya5ki_CjTKaCuhaKmLon1QLYV-KVUrdfKTBg0FB1HEG1QPS2gNNCCpqGlOaNWCVxFitnlqZQcyJur9d80tL8Nf9Frcm66rjXthUFvP7ZBdhgy6BIvbN_rytmo9nR3tFO-vqJO7nm/https%3A%2F%2Fwww.illumina.com%2Fproducts%2Fby-type%2Fmicroarray-kits%2Finfinium-methylation-epic.html) and currently there is no manifest nor annotation packages for that one. The available packages on Bioconductor are only for EPIC array v1.0: - IlluminaHumanMethylationEPICmanifest - IlluminaHumanMethylationEPICanno.ilm10b4.hg19 And it is not proper to use the v1 packages for the v2 data. I've built a manifest package and an annotation package for the EPIC array v2.0. They are available at: https://secure-web.cisco.com/1QiOF2zfvxn-NM_D59JEGrLZNxfjlhE96RB2QFStOhZ-M_vbiO6U4EAWhA4DxQl2K4UCyCR2IlwPHsInzW3sJ2AMU8ZGdfx2iG9GgacdRqfiLFso1I8byAAr3GSfV0yC6vYlWWOAcemIIiQmhz2ucGFBPnr6_XM6d-Fu8yoDbXBs4Kgr-BcAl-Pd75iP9-5p892EmkkdxAoDV7gLycQbrWXkoZ_k4OFitm-jojHDyBux8UbuaxsY6o_AM-f-5uji4V325my36EKUam9Fs_BWlQuoEm92wkvrPfLOrfSGs3gNRe_yOUL-xnZE2dgDIlwr_/https%3A%2F%2Fgithub.com%2Fjokergoo%2FIlluminaHumanMethylationEPICv2manifest https://secure-web.cisco.com/1cO_2hmhoc2EdgBhXjFVHzLhg8R28yb3KFaT2NGVp8p93xKzA8PkG-N2DaTdM1tL75mwBskP9Kd-h2MLGiXL85Pfa8uZd6kt11AoYZjhV6ndx7tUFMKrg3Sk4xT-JqpFRKzZe-ZRCbxOZmeF5yN_MNrKtHMi2mb4jSjbH2dsyG4kKc5CsuTh7xJZV91XBDkTbss0G5a2iD_kkpBLsxMAZz8xA5HK7kQBjUJl-fxgJ5-VyNeEuyXCUKbsI3JTNby7p6xyfjXyIBGZRyuCc5Vbr3bAnpChMyTfiSmvQmjLRn3_uUdnJp9FoAwBye9Y2_M6G/https%3A%2F%2Fgithub.com%2Fjokergoo%2FIlluminaHumanMethylationEPICv2anno.20a1.hg38 Basically they are built with the scripts in the original v1 packages, with small adjustment. The scripts for building the two packages are also included in the two packages. The two v2 packages can be seamlessly integrated into the minfi analysis. I also did some simple comparisons between v1 and v2 ( https://secure-web.cisco.com/1tb2XcerFPyKtnWDHASWp4HiJmKkEZQnpQRX0pCr4zdfYKshBWou5hiaQCMU7fxctqgxTJZHcVXeMDCsdYO4DKDTFGvXu1plvlZqOlJL_XL6wrom9PLgn0bYaqHp3f0gwbDwdR6DndCxxxmy7W8prmtZDI4h4hA_zpjZAQXUS3C77vrKmAB0L2oS_JxbGROozS9GRKkh2dTon2-KX8gl0DDiSGfbubl7xv2mtCcwLhlCW-cQ4W5zpEb7wIk7j1uqvHdAC-jwsG9VPm8VyThNbkBNrijwdrCIfHuggvBKfSknu0oFR42VZ9ifm6JaY3GTm/https%3A%2F%2Fjokergoo.github.io%2FIlluminaHumanMethylationEPICv2manifest%2Farticles%2FIlluminaHumanMethylationEPICv2manifest.html ). Since the v1 packages were developed by the bioc core members, I want to ask is there any plan to support the EPIC v2 array officially? If there is no such plan, can I submit the two packages to bioc? If I can, then I will have some additional questions regarding how to pass BiocCheck (e.g. file size, lazy loading, ...). But that will be in another email. Best, Zuguang [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1fLuxP9yMKjXXVX4U5tHzgq75S4SiNaqqCjLqVieInk0UcUFlM9Awx7EvllsKfkmUEniVGH9qtKoo7YszKjXKiEqBmS-SnNM5_w5UYUkpy_dra04LGCCNrmlmTbGxHsBYUbisl9F6Yap5oDm92TIPyqi1KON0yYy85JJ0laeEbH6hsT4RUGa7NgW2PBNm7lUnl0z7ryA7jU-y2g0Vxq4r43sbbuCtkxrL23V_MwiMsRq3ekTwtHudDEoUNxJurdguVYJRzxPP4Ji4f7U5SucexI2cYfMIDl2e3Puple98Zuo9MxVTEYXpZ-nLJgqVe7LS/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. 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