bioconductor / csama Goto Github PK
View Code? Open in Web Editor NEWCourse material for CSAMA: Statistical Data Analysis for Genome Scale Biology
Home Page: https://csama2024.bioconductor.eu/
Course material for CSAMA: Statistical Data Analysis for Genome Scale Biology
Home Page: https://csama2024.bioconductor.eu/
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:
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:
AnnotationDbi
, org.*
, AnnotationHub
, biomaRt
, ...) similar to https://github.com/Bioconductor/BiocIntro/blob/Technion-2016/vignettes/S6_Annotation_and_performance.Rmd, Annotation section.ensembldb
:
ensembldb
intro.AnnotationFilter
intro.EnsDb
s.EnsDb
packages.EnsDb
and AnnotationDbi
.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Also, @mikelove and @csoneson I'd appreciate your input on this lab - especially since I'm no longer active in transcriptome stuff: so feel free to edit and modify the annotation-with-ensembldb.Rmd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:
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!
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.