[BioC] Course material for "Using Bioconductor for ChIP-seq experiments"

Patrick Aboyoun paboyoun at fhcrc.org
Thu Nov 20 22:29:26 CET 2008

The course material for "Using Bioconductor for ChIP-seq experiments", 
which was held at the Fred Hutchinson Cancer Research Center from 12-14 
Nov 2008, is now available on-line at


Topics for this course include:

   1. Overview of Bioconductor and high-throughput sequence data
   2. Sequence Data I/O and QA using ShortRead
   3. Sequence Data Exploration using rtracklayer
   4. Sequence Data Annotations from org.* packages and biomaRt package
   5. Biostrings and BSgenome Basics
   6. Sequence Matching and Aligning using Biostrings
   7. Ambiguous Motif Resolution
   8. Example ChIP-seq Analysis Workflow
   9. RNA-seq

This course was designed to highlight what BioC 2.3, along with R 2.8, 
has to offer experimenters working with high-throughput sequence data. 
Course participants used laptop computers to read, examine, annotate, 
align, and analyze high-throughput sequence data on the BioC 2.3 
ShortRead/Biostrings/BSgenome/IRanges/rtracklayer/biomaRt backbone. 
Members of the Bioconductor Core Team that attended the course are 
thankful for all the feedback they received from these participants and 
they are actively converting this feedback into enhancements within the 
BioC 2.4 code line. Please direct all comments on this course material 
as well as BioC 2.4 enhancement requests in the sequencing realm to the 
Bioc-sig-sequencing group 
(https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing) since it 
provides a forum for more detailed discussion by interested parties.

The Bioconductor Core Team

More information about the Bioconductor mailing list