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

RNA-Seq

Sequencing the transcriptome