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Describes how to use the csaw package to detect differentially bound regions in ChIP-seq data. This provides instructions on how to read in BAM files to obtain a per-window count matrix, filtering to obtain high-abundance windows of interest, normalization of sample-specific biases, testing for differential binding, consolidation of per-window results to obtain per-region statistics, and annotation and visualization of the DB results.
Author: Aaron Lun Maintainer: Aaron Lun License: GPL-3
The primary aim of this book is to introduce the R user to Hi-C analysis. This book starts with key concepts important for the analysis of chromatin conformation capture and then presents Bioconductor tools that can be leveraged to process, analyze, explore and visualize Hi-C data.
Author: Jacques Serizay Maintainer: Jacques Serizay License: MIT + file LICENSE
Online book for orchestrating single cell analysis with Bioconductor. Contains plenty of worked examples, theoretical background and some philosophical discussions on the nature of single-cell data analysis.
Authors: Robert Amezquita, Aaron Lun, Stephanie Hicks, Raphael Gottardo, Alan O'Callaghan Maintainer: Alan O'Callaghan License: CC BY 4.0
Comprehensive guide to using the SingleR Bioconductor package for automated cell annotation in single-cell RNA-seq datasets. Includes theoretical explanations, worked examples with code, and demonstrations of advanced functionality
Author: Aaron Lun Maintainer: Aaron Lun License: CC BY
A demo of a BiocBook online book.
