\contentsline {section}{\numberline {1}Introduction}{2}{section.1}
\contentsline {subsection}{\numberline {1.1}\textsl {Rstudio}}{2}{subsection.1.1}
\contentsline {subsection}{\numberline {1.2}\textsl {R}}{2}{subsection.1.2}
\contentsline {subsection}{\numberline {1.3}\textsl {Bioconductor}}{3}{subsection.1.3}
\contentsline {paragraph}{High-throughput sequence analysis}{4}{section*.2}
\contentsline {subsection}{\numberline {1.4}Resources}{4}{subsection.1.4}
\contentsline {section}{\numberline {2}Sequences and Ranges}{5}{section.2}
\contentsline {subsection}{\numberline {2.1}{\href {http://bioconductor.org/packages/release/bioc/html/Biostrings.html} {\textsl {Biostrings}}}}{5}{subsection.2.1}
\contentsline {subsection}{\numberline {2.2}{\href {http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html} {\textsl {GenomicRanges}}}}{5}{subsection.2.2}
\contentsline {paragraph}{\textit {GRanges}}{5}{section*.3}
\contentsline {paragraph}{Operations on ranges}{6}{section*.4}
\contentsline {paragraph}{{\texttt {mcols}}}{6}{section*.5}
\contentsline {paragraph}{\textit {GRangesList}}{7}{section*.6}
\contentsline {paragraph}{The {\href {http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html} {\textsl {GenomicFeatures}}} package}{8}{section*.7}
\contentsline {subsection}{\numberline {2.3}Resources}{9}{subsection.2.3}
\contentsline {section}{\numberline {3}Reads and Alignments}{10}{section.3}
\contentsline {subsection}{\numberline {3.1}The \emph {pasilla} Data Set}{10}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Reads and the {\href {http://bioconductor.org/packages/release/bioc/html/ShortRead.html} {\textsl {ShortRead}}} Package}{10}{subsection.3.2}
\contentsline {paragraph}{Short read formats}{10}{section*.8}
\contentsline {subsection}{\numberline {3.3}Alignments and the {\href {http://bioconductor.org/packages/release/bioc/html/Rsamtools.html} {\textsl {Rsamtools}}} Package}{12}{subsection.3.3}
\contentsline {paragraph}{Alignment formats}{13}{section*.9}
\contentsline {paragraph}{Aligned reads in \textsl {R}{}}{13}{section*.10}
\contentsline {section}{\numberline {4}RNA-seq}{16}{section.4}
\contentsline {paragraph}{Varieties of RNA-seq}{16}{section*.11}
\contentsline {subsection}{\numberline {4.1}Differential Expression with the {\href {http://bioconductor.org/packages/release/bioc/html/edgeR.html} {\textsl {edgeR}}} Package}{16}{subsection.4.1}
\contentsline {paragraph}{Counting and filtering}{16}{section*.12}
\contentsline {paragraph}{Experimental design}{17}{section*.13}
\contentsline {paragraph}{Negative binomial error}{18}{section*.14}
\contentsline {paragraph}{Differential representation}{18}{section*.15}
\contentsline {subsection}{\numberline {4.2}Additional Steps in RNA-seq Work Flows}{19}{subsection.4.2}
\contentsline {subsection}{\numberline {4.3}Resources}{19}{subsection.4.3}
\contentsline {section}{\numberline {5}ChIP-seq}{20}{section.5}
\contentsline {subsection}{\numberline {5.1}Initial Work Flow}{20}{subsection.5.1}
\contentsline {subsection}{\numberline {5.2}Motifs}{22}{subsection.5.2}
\contentsline {paragraph}{Known binding motifs}{22}{section*.16}
\contentsline {section}{\numberline {6}Annotation}{24}{section.6}
\contentsline {subsection}{\numberline {6.1}Gene-Centric Annotations with {\href {http://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html} {\textsl {AnnotationDbi}}}}{24}{subsection.6.1}
\contentsline {subsection}{\numberline {6.2}Genome-Centric Annotations with {\href {http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html} {\textsl {GenomicFeatures}}}}{25}{subsection.6.2}
\contentsline {subsection}{\numberline {6.3}Exploring Annotated Variants: {\href {http://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html} {\textsl {VariantAnnotation}}}}{28}{subsection.6.3}
