bioconductor / csama Goto Github PK

The .git for this repo is 1.8 Gb which is prohibitive to clone at the course (wifi is typically slow). The current lecture directory of CSAMA itself contains 649 Mb of material.

Suggest to deprecate this repo and instead use CSAMA-labs with a separate location for the lecture content. We used Google Drive in 2024 for lectures.

The CSAMA-labs repo contains the labs from 2024 and has a .git of 35 Mb.

➜  CSAMA-labs git:(devel) ✗ du -sh * | sort -h
4.0K	README.md
8.0K	scripts
860K	bulk-atacseq
3.4M	bulk-rnaseq
4.0M	quarto-intro
7.0M	single-cell-rnaseq
8.1M	multicond-scRNA-lemur
 11M	intro-to-r-bioc
 12M	spatial-transcriptomics

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?

should be 17-06?

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?

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Also, @mikelove and @csoneson I'd appreciate your input on this lab - especially since I'm no longer active in transcriptome stuff: so feel free to edit and modify the annotation-with-ensembldb.Rmd.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

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

@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)?

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