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