Bioconductor Online Books

The csaw Book

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 <infinite.monkeys.with.keyboards@gmail.com>

License: GPL-3

Orchestrating Single-Cell Analysis with Bioconductor

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

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>

License: CC BY-NC-ND 3.0 US

Assigning cell types with SingleR

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 <infinite.monkeys.with.keyboards@gmail.com>

License: CC BY