Bioconductor Online Books

Bioconductor version: 3.19

IMPORTANT NOTE: This is NOT the current release! See here for the most current versions of the 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