I can assist you with this request. In the future there is the email h...@bioconductor.org for these types of requests instead of the developer mailing list as mentioned in the documentation.
I'll contact you off mailing list for further details and instruction. 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 Sara López Ruiz de Vargas <lope...@molgen.mpg.de> Sent: Wednesday, April 24, 2024 9:17 AM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [Bioc-devel] New annotation hub package? Dear developers community, We are currently developing a package for which we are quite sure we will need a supporting AnnotationHub or ExperimentHub package to go with it. We are using a set of gene annotations (GENCODE version 40 hg38) and enhancer annotations (ENCODE registry of cCREs v3), which are not available in the AnnotationHub. Correct me if I’m wrong. On top of that, our package depends on in house precomputed datasets that occupy a lot of space. We have solved this issue temporarily by making the annotations and the precomputed data into RSQLite databases which the user can download (into inst/extada) once the package is installed. This however makes the inst/extdata folder really large (above 5GB). Most likely a Hub package would be a better solution. When looking at the documentation ( https://secure-web.cisco.com/1SsSYiZvjhKsQTFDCiJs0zb6X29DjrpzlJ2hbWrRlx8i-tJpOM_X_CeJJbTIno7lpn5KpG38T0R-RtgcpXEhht9UGyKnVc-Xhzfc7uJKGpjgkNWPgaAqEkv7dtSBqHZjisJHne-FoHtc3puPdivFQ5JoxHenR3tMndo8F4AxdcaDrmc86qyiC7wulOGvXG8urAj43FaLkpCC-GQSWFFCeqaN6Bj55ech4IoyaCMU0cfKv70FAKXhk1dTjtQjDe9e8SxKEhdSipEWpUWIsk-QnozRWMFNRit5mLBhjgQzTW60FMWumv_ztFHv9Zhl1YhgZ/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fvignettes%2FHubPub%2Finst%2Fdoc%2FCreateAHubPackage.html ) one of the first things mentioned is to contact a Bioconductor team member. I was wondering if I could find someone in this forum who could help with this. Best regards, Sara Lopez -- Sara López Ruiz de Vargas Max Planck Institute for Molecular Genetics Vingron Lab / Dept. of Computational Molecular Biology Ihnestraße 63-73 14195 Berlin GERMANY _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/19y5jjNThFPctQlUbT6K3Hg9mlaxJVmKPEEjbx1GABHcgiaZQLDwUslfiGwqVxEnsyORtZigkAfhFetbn6fqOLCK8y1y2W7c7TL_aqCedQIJ5FNhIQndxPaGaMUo0FACODWPqqZdSC6mh3lYOeOKBsF_Nj2dYROxddjkqPgYIeDqPjsQrusThRWvpl0X_WYU5w-fAsPWm-96kj-SbyCdQn06KfZukOoWr4X2bp1PKqn352I2YAKsTfyaeDAj56glb4YClnSN8ON42U_W1gVe--tk1h65kVazU_2Flfv-1AmhBNg60B7Rppzv99K_b44eS/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
