Bioinformatics with R Cookbook -- Table of Contents -- Bioinformatics with R Cookbook -- Credits -- About the Author -- About the Reviewers -- www.PacktPub.com -- Support files, eBooks, discount offers, and more -- Why Subscribe? -- Free Access for Packt account holders -- Preface -- What this book covers -- What you need for this book -- Who this book is for -- Conventions -- Reader feedback -- Customer support -- Downloading the example code -- Downloading the color images of this book -- Errata -- Piracy -- Questions -- 1. Starting Bioinformatics with R -- Introduction -- Getting started and installing libraries -- Getting ready -- How to do it… -- How it works... -- There's more... -- Reading and writing data -- Getting ready -- How to do it… -- How it works… -- There's more… -- Filtering and subsetting data -- Getting ready -- How to do it… -- How it works… -- There's more… -- Basic statistical operations on data -- Getting ready -- How to do it… -- How it works… -- Generating probability distributions -- How to do it… -- How it works… -- There's more… -- Performing statistical tests on data -- How to do it… -- How it works… -- There's more… -- Visualizing data -- Getting ready -- How to do it… -- How it works… -- There's more… -- Working with PubMed in R -- Getting ready -- How to do it… -- How it works… -- Retrieving data from BioMart -- Getting ready -- How to do it… -- How it works… -- There's more… -- See also -- 2. Introduction to Bioconductor -- Introduction -- Installing packages from Bioconductor -- Getting ready -- How to do it… -- How it works… -- There's more... -- Handling annotation databases in R -- Getting ready -- How to do it… -- How it works… -- There's more… -- Performing ID conversions -- Getting ready -- How to do it… -- How it works… -- There's more… -- The KEGG annotation of genes -- Getting ready -- How to do it….

How it works… -- There's more… -- The GO annotation of genes -- Getting ready -- How to do it… -- How it works… -- There's more… -- See also -- The GO enrichment of genes -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- The KEGG enrichment of genes -- Getting ready -- How to do it… -- How it works... -- See also -- Bioconductor in the cloud -- Getting ready -- How to do it… -- How it works… -- See also -- 3. Sequence Analysis with R -- Introduction -- Retrieving a sequence -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- Reading and writing the FASTA file -- Getting ready -- How to do it… -- How it works… -- See also -- Getting the detail of a sequence composition -- Getting ready -- How to do it… -- How it works… -- See also -- Pairwise sequence alignment -- Getting ready -- How to do it… -- How it works… -- See also -- Multiple sequence alignment -- Getting ready -- How to do it… -- How it works… -- See also -- Phylogenetic analysis and tree plotting -- Getting ready -- How to do it… -- How it works… -- See also -- Handling BLAST results -- Getting ready -- How to do it… -- How it works… -- See also -- Pattern finding in a sequence -- Getting ready -- How to do it… -- How it works… -- See -- 4. Protein Structure Analysis with R -- Introduction -- Retrieving a sequence from UniProt -- Getting ready -- How to do it… -- How it works… -- See also -- Protein sequence analysis -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- Computing the features of a protein sequence -- Getting ready -- How to do it… -- How it works… -- See also -- Handling the PDB file -- Getting ready -- How to do it… -- How it works… -- Working with the InterPro domain annotation -- Getting ready -- How to do it… -- How it works... -- There's more... -- See also.

Understanding the Ramachandran plot -- Getting ready -- How to do it… -- How it works… -- See also -- Searching for similar proteins -- Getting ready -- How to do it… -- How it works… -- Working with the secondary structure features of proteins -- Getting ready -- How to do it… -- How it works… -- Visualizing the protein structures -- Getting ready -- How to do it… -- How it works… -- 5. Analyzing Microarray Data with R -- Introduction -- Reading CEL files -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- Building the ExpressionSet object -- Getting ready -- How to do it… -- How it works… -- Handling the AffyBatch object -- Getting ready -- How to do it… -- How it works… -- Checking the quality of data -- Getting ready -- How to do it… -- How it works… -- Generating artificial expression data -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- Data normalization -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- Overcoming batch effects in expression data -- Getting ready -- How to do it… -- How it works… -- See also -- An exploratory analysis of data with PCA -- Getting ready -- How to do it… -- How it works… -- See also -- Finding the differentially expressed genes -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- Working with the data of multiple classes -- Getting ready -- How to do it… -- How it works… -- Handling time series data -- Getting ready -- How to do it… -- How it works… -- There's more... -- Fold changes in microarray data -- Getting ready -- How to do it… -- How it works… -- The functional enrichment of data -- Getting ready -- How to do it… -- How it works… -- There's more... -- Clustering microarray data -- Getting ready -- How to do it… -- How it works… -- There's more...

Getting a co-expression network from microarray data -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- More visualizations for gene expression data -- Getting ready -- How to do it… -- How it works… -- 6. Analyzing GWAS Data -- Introduction -- The SNP association analysis -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- Running association scans for SNPs -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- The whole genome SNP association analysis -- Getting ready -- How to do it… -- How it works… -- There's more... -- Importing PLINK GWAS data -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- Data handling with the GWASTools package -- Getting ready -- How to do it... -- How it works… -- See also -- Manipulating other GWAS data formats -- Getting ready -- How to do it… -- How it works… -- See also -- The SNP annotation and enrichment -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- Testing data for the Hardy-Weinberg equilibrium -- Getting ready -- How to do it… -- How it works… -- See also -- Association tests with CNV data -- Getting ready -- How to do it… -- How it works… -- There's more... -- Visualizations in GWAS studies -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- 7. Analyzing Mass Spectrometry Data -- Introduction -- Reading the MS data of the mzXML/mzML format -- Getting ready -- How to do it… -- How it works… -- See -- Reading the MS data of the Bruker format -- Getting ready -- How to do it… -- How it works… -- See also -- Converting the MS data in the mzXML format to MALDIquant -- Getting ready -- How to do it… -- How it works… -- See also -- Extracting data elements from the MS data object -- Getting ready -- How to do it….

How it works… -- There's more… -- See also -- Preprocessing MS data -- Getting ready -- How to do it… -- How it works… -- See also -- Peak detection in MS data -- Getting ready -- How to do it… -- How it works… -- See also -- Peak alignment with MS data -- Getting ready -- How to do it… -- How it works… -- There's more... -- Peptide identification in MS data -- Getting ready -- How to do it… -- How it works… -- There's more… -- See also -- Performing protein quantification analysis -- Getting ready -- How to do it… -- How it works… -- See also -- Performing multiple groups' analysis in MS data -- Getting ready -- How to do it… -- How it works… -- See also -- Useful visualizations for MS data analysis -- Getting ready -- How to do it… -- How it works… -- 8. Analyzing NGS Data -- Introduction -- Querying the SRA database -- Getting ready -- How to do it… -- How it works… -- See also -- Downloading data from the SRA database -- Getting ready -- How to do it… -- How it works… -- Reading FASTQ files in R -- Getting ready -- How to do it… -- How it works… -- See also -- Reading alignment data -- Getting ready -- How to do it… -- How it works… -- See also -- Preprocessing the raw NGS data -- Getting ready -- How to do it… -- How it works… -- There's more... -- Analyzing RNAseq data with the edgeR package -- Getting ready -- How to do it… -- How it works… -- See also -- The differential analysis of NGS data using limma -- Getting ready -- How to do it… -- How it works… -- See also -- Enriching RNAseq data with GO terms -- Getting ready -- How to do it… -- How it works… -- There's more... -- See also -- The KEGG enrichment of sequence data -- Getting ready -- How to do it… -- How it works… -- Analyzing methylation data -- Getting ready -- How to do it… -- How it works… -- See also -- Analyzing ChipSeq data -- Getting ready -- How to do it… -- How it works….

See also.