https://github.com/jorainer/eurobioc2016-ensembldb

Material for the European Bioconductor Developer's Meeting 2016 in Basel, Switzerland
https://github.com/jorainer/eurobioc2016-ensembldb

Last synced: 3 months ago
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Material for the European Bioconductor Developer's Meeting 2016 in Basel, Switzerland

• Host: GitHub
• URL: https://github.com/jorainer/eurobioc2016-ensembldb
• Owner: jorainer
• Created: 2016-10-19T05:35:31.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-12-06T21:20:04.000Z (over 8 years ago)
• Last Synced: 2025-01-20T22:54:59.200Z (5 months ago)
• Language: R
• Size: 313 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: readme.org

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README

        
Repository providing my material for the [[http://scicore.ch/events/eurobioc2016/][European Bioconductor Developer's

Meeting 2016]] in Basel, Switzerland.

As of December 2016 developmental package versions of =ensembldb= and =Pbase= were

used (https://github.com/jotsetung/ensembldb and

https://github.com/ComputationalProteomicsUnit/Pbase/tree/ensembldb , /ensembldb/ branch).

+ The presentation (as Emacs org-mode file): [[file:EuroBioC2016-ensembldb.org]].

+ The presentation formatted for org-mode to beamer export: [[file:EuroBioC2016-ensembldb-beamer.org]].

Beamer presentation pdf: [[file:EuroBioC2016-ensembldb-beamer.pdf]].

Some notes on my emacs setup:

+ Theme: https://github.com/jotsetung/flatui-emacs.

+ /Bullets/ instead of /*/ (stars): https://github.com/sabof/org-bullets.

+ The whole package: https://github.com/jotsetung/memacs

* TODOs								   :noexport:

** DONE Write abstract

   CLOSED: [2016-11-16 Wed 09:18]

   - State "DONE"       from "TODO"       [2016-11-16 Wed 09:18]

** DONE Create the presentation [10/10]

   CLOSED: [2016-12-04 Sun 18:57]

   - State "DONE"       from "TODO"       [2016-12-04 Sun 18:57]

+ [X] General introduction

+ [X] Database layout with http://asciiflow.com/

+ [X] Simple examples to fetch genes/transcripts: show filters.

+ [X] Create databases: ideally using Perl API.

+ [X] Create mysql database.

  - Benefit: have one central dedicated server for all EnsDbs.

  - Performance gain if MySQL configured properly.

+ [X] Integrate with UCSC annotations. -> things not covered?

+ [X] Fetch protein data: the =proteins= method.

+ [X] Using =select=. -> things not covered?

+ [X] Integration into =Pbase=.

+ [X] Map peptide features to chromosome.