\BOOKMARK [1][]{section.1}{1 Introduction}{}% 1
\BOOKMARK [2][]{subsection.1.1}{1.1 Rstudio}{section.1}% 2
\BOOKMARK [2][]{subsection.1.2}{1.2 R}{section.1}% 3
\BOOKMARK [2][]{subsection.1.3}{1.3 Bioconductor}{section.1}% 4
\BOOKMARK [2][]{subsection.1.4}{1.4 Resources}{section.1}% 5
\BOOKMARK [1][]{section.2}{2 Sequences and Ranges}{}% 6
\BOOKMARK [2][]{subsection.2.1}{2.1 Biostrings}{section.2}% 7
\BOOKMARK [2][]{subsection.2.2}{2.2 GenomicRanges}{section.2}% 8
\BOOKMARK [2][]{subsection.2.3}{2.3 Resources}{section.2}% 9
\BOOKMARK [1][]{section.3}{3 Reads and Alignments}{}% 10
\BOOKMARK [2][]{subsection.3.1}{3.1 The pasilla Data Set}{section.3}% 11
\BOOKMARK [2][]{subsection.3.2}{3.2 Reads and the ShortRead Package}{section.3}% 12
\BOOKMARK [2][]{subsection.3.3}{3.3 Alignments and the Rsamtools Package}{section.3}% 13
\BOOKMARK [1][]{section.4}{4 RNA-seq}{}% 14
\BOOKMARK [2][]{subsection.4.1}{4.1 Differential Expression with the edgeR Package}{section.4}% 15
\BOOKMARK [2][]{subsection.4.2}{4.2 Additional Steps in RNA-seq Work Flows}{section.4}% 16
\BOOKMARK [2][]{subsection.4.3}{4.3 Resources}{section.4}% 17
\BOOKMARK [1][]{section.5}{5 ChIP-seq}{}% 18
\BOOKMARK [2][]{subsection.5.1}{5.1 Initial Work Flow}{section.5}% 19
\BOOKMARK [2][]{subsection.5.2}{5.2 Motifs}{section.5}% 20
\BOOKMARK [1][]{section.6}{6 Annotation}{}% 21
\BOOKMARK [2][]{subsection.6.1}{6.1 Gene-Centric Annotations with AnnotationDbi}{section.6}% 22
\BOOKMARK [2][]{subsection.6.2}{6.2 Genome-Centric Annotations with GenomicFeatures}{section.6}% 23
\BOOKMARK [2][]{subsection.6.3}{6.3 Exploring Annotated Variants: VariantAnnotation}{section.6}% 24
