Coding Club

We are excited with our ongoing LeedsOmics Coding Club (LOCC) sessions, an open and friendly space where you can bring all your omics analytical issues to discussion on a biweekly meeting series. Thanks for all those who have attended and contributed to the club, enriching our chat. It has been great! Please check out the introductory slides we prepared for each session: ggplot2 for nice charts; Good practice in writing code; Basic statistics within R; Accessing & downloading data from online DBs; Dealing with NGS data; Regular expression and pattern search;

We are organising club sessions by broad themes that LeedsOmics community might be interested in. Therefore, we launched a survey on specific topics which researchers may want to chat on. The chart below depicts the result from that survey sorted by percentage of people interested. As agreed, LOCC sessions’ order will follow that result. Our next session will then be on “Command line – navigating directories, creating/editing files & file management” on Monday, 25/11/2019 at 2:15 in Garstang SR (7.52). Hope to see you there!

There were also other topics suggested by survey participants, which are the following:

  • Comparing translational efficiency between different datasets (eg Control-treatment) (Bayesian or other approaches);
  • Extracting RNA-seq / CLIP-seq from publicly available databases;
  • Systematically investigate synteny across different species and infer the location of a gene on one chromosome in species A relative to a species B;
  • Use phyloP to get conservation representation schematics, since people may value these more than identity matrix scores;
  • Mutation calling
  • Co-expression networks: generation and interpretation

Please feel free to drop us an email anytime with more suggestions on topics to be covered (fbsev@leeds.ac.uk).

NOTE: Please bear in mind that the Coding Club is not supposed to be a tutorial on how to perform bioinformatic analyses from the scratch. You are expected to have already started your analysis, investigate the theme on your own, and then bring your issues to sessions. Your issues can be either doubts/frustrations during your coding process or comments/hints on best practices in your analyses.

Looking forward to seeing you at the club,

Sincerely,

Elton Vasconcelos (organizer)

LOCC moderators team: Peter Mulhair, Euan McDonnell, Chew Cheng,
Dapeng Wang, and Elton Vasconcelos

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