I'd need the topTable from the RNAseq workflow to start with the annotation part (@mikelove, @csoneson could you provide that at some point?)

Also, @mikelove and @csoneson I'd appreciate your input on this lab - especially since I'm no longer active in transcriptome stuff: so feel free to edit and modify the annotation-with-ensembldb.Rmd.

Additional things I thought we could include is:

• Search for transcripts that encode proteins with a certain protein domain, such as the steroid receptor ligand binding domain (that also the glucocorticoid receptor has).
• If we have e.g. an alignment of an sequence read within a transcript, we could use ensembldb to convert that coordinates to genome- or protein-relative coordinates.

Would an administrator please provide me with push access? Thanks!

I have one data file that is too large. From /CSAMA/lab/4-thursday/lab-04-Mass_spec_proteomics_and_metabolomics/01-proteomics/data/README:

There is only file, namely

  TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML

that is too large for git, which will need to be copied manually on the
local server.

Cc @grimbough

For the metabolomics part I planned to show:

• Data import, organization and handling (read data, access spectra, extract chromatogram, simple QC).
• Chromatographic peak detection
• Alignment/retention time correction
• Correspondence (grouping of chromatographic peaks across samples)
• Exploring feature data (simple PCA, ev. diff exp etc).

So, in principle this just handles the pre-processing that can be done with xcms and presenting the new capabilities of xcms (XCMSnExp object extending the OnDiskMSnExp, Chromatogram class etc). For time reasons I would not go into normalization, signal drift adjustment and metabolite identification.

@lgatto , I thought of putting all that stuff into a separate Rmd. We might decide to fuse your and my Rmd, but I think the topics are too different.

@lgatto what you think of that?

@lgatto would it be OK for you to split the lecture into 35 and 20 minute parts (first part your proteomics, second part my metabolomics)?

Was already thinking about the content for the Annotation resources lecture for CSAMA2017.

My proposal would be:

• First part (~ 30 minutes): @mtmorgan with a general overview (AnnotationDbi, org.*, AnnotationHub, biomaRt, ...) similar to https://github.com/Bioconductor/BiocIntro/blob/Technion-2016/vignettes/S6_Annotation_and_performance.Rmd, Annotation section.
• Second part (~ 15 minutes): @jotsetung with ensembldb:
  • ensembldb intro.
  • AnnotationFilter intro.
  • filtering EnsDbs.
  • building/getting EnsDb packages.
  • EnsDb and AnnotationDbi.
  • protein annotations with ensembldb.

@mtmorgan , what do you think?

should be 17-06?