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Using Bioconductor for ChIP-seq experiments

Bioconductor Overview
Using Bioconductor with high-throughput sequence data
Sequence Data I/O and QA using ShortRead
Using ShortRead to perform I/O and QA of high throughput sequence data
Sequence Data Exploration using rtracklayer
Using rtracklayer to visualize sequence data with annotations
Sequence Data Annotations
Using org.* annotation packages and biomaRt to get annotations about sequence data
Biostrings and BSgenome Basics
Basics of the Biostrings, BSgenome, and IRanges packages
Sequence Matching & Aligning using Biostrings
Using Biostrings to match and align sequences
Ambiguous Motifs Resolution
Resolving ambiguous motifs with ChIP-seq
Example ChIP-seq Analysis Workflow
Example workflow for a particular ChIP-seq analysis
Sequencing the transcriptome