https://github.com/Bioconductor/UseBioconductor

Training material for intermediate R / Bioconductor courses
https://github.com/Bioconductor/UseBioconductor

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Training material for intermediate R / Bioconductor courses

• Host: GitHub
• URL: https://github.com/Bioconductor/UseBioconductor
• Owner: Bioconductor
• Created: 2015-01-28T21:13:32.000Z (almost 10 years ago)
• Default Branch: devel
• Last Pushed: 2023-03-15T20:25:40.000Z (over 1 year ago)
• Last Synced: 2024-06-07T19:48:31.471Z (6 months ago)
• Language: R
• Homepage:
• Size: 4.28 MB
• Stars: 17
• Watchers: 20
• Forks: 6
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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• awesome-bacteria - UseBioconductor - Use R / Bioconductor for Sequence Analysis (2015). (Educational resources / Bioconductor)

README

        
Use R / Bioconductor for Sequence Analysis

==========================================

Fred Hutchinson Cancer Research Center, Seattle, WA


6-7 April, 2015

Contact: Martin Morgan

([[email protected]](mailto:[email protected]))

This **INTERMEDIATE** course is designed for individuals comfortable

using _R_, and with some familiarity with _Bioconductor_. It consists

of approximately equal parts lecture and practical sessions addressing

use of _Bioconductor_ software for analysis and comprehension of

high-throughput sequence and related data. Specific topics include use

of central Bioconductor classes (e.g., _GRanges_,

_SummarizedExperiment_), RNASeq gene differential expression, ChIP-seq

and methylation work flows, approaches to management and integrative

analysis of diverse high-throughput data types, and strategies for

working with large data. Participants are required to bring a laptop

with wireless internet access and a modern version of the Chrome or

Safari web browser.

Registration

------------

Please register [online](https://register.bioconductor.org/Seattle-Apr-2015/).

Schedule (tentative)

--------------------

Day 1 (9:00 - 12:30; 1:30 - 5:00)

- [A. Introduction](vignettes/A_Introduction.Rmd). _Bioconductor_ and

  sequencing work flows

- [B. Genomic Ranges](vignettes/B_GenomicRanges.Rmd). Working with Genomic

  Ranges and other _Bioconductor_ data structures (e.g., in the

  [GenomicRanges](http://bioconductor.org/packages/devel/bioc/html/GenomicRanges.html).

  package).  

- [C. Differential Gene Expression](vignettes/C_DifferentialExpression.Rmd). RNA-Seq

  known gene differential expression with

  [DESeq2](http://bioconductor.org/packages/devel/bioc/html/DESeq2.html)

  and

  [edgeR](http://bioconductor.org/packages/devel/bioc/html/edgeR.html).

Day 2 (9:00 - 12:30; 1:30 - 5:00)

- [D. Machine Learning](vignettes/D_MachineLearning.Rmd).

- [E. Gene Set Enrichment](vignettes/E_GeneSetEnrichment.Rmd).

- [F. ChIP-seq](vignettes/F_ChIPSeq.Rmd) ChIP-seq with

  [csaw](http://bioconductor.org/packages/devel/bioc/html/csaw.html)

- [I. Large Data](vignettes/I_LargeData.Rmd) -- efficient, parallel, and cloud

  programming with

  [BiocParallel](http://bioconductor.org/packages/devel/bioc/html/BiocParallel.html),

  [GenomicFiles](http://bioconductor.org/packages/devel/bioc/html/GenomicFiles.html),

  and other resources.