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MacLean, Dan. R Bioinformatics Cookbook: Use R and Bioconductor to Perform RNAseq, Genomics, Data Visualization, and Bioinformatic Analysis. — Birmingham: Packt Publishing, Limited, 2019. — 1 online resource (307 pages) — <URL:http://elib.fa.ru/ebsco/2272987.pdf>.

Дата создания записи: 26.10.2019

Тематика: Bioinformatics.; R (Computer program language); Computational biology.; Bio-informatique.; R (Langage de programmation); Bioinformatics.; R (Computer program language)

Коллекции: EBSCO

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Аннотация

In the R Bioinformatics Cookbook, you encounter common and not-so-common challenges in the bioinformatics domain and solve them using real-world examples. The book guides you through varied bioinformatics analysis, from raw data to clean results. It shows you how to import, explore and evaluate your data and how to report it.

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Cover
Title Page
Copyright and Credits
About Packt
Contributors
Table of Contents
Preface
Chapter 1: Performing Quantitative RNAseq
- Technical requirements
- Estimating differential expression with edgeR
  - Getting ready
  - How to do it...
    - Using edgeR from a count table
    - Using edgeR from an ExpressionSet object
  - How it works...
    - Using edgeR from a count table
    - Using edgeR from an ExpressionSet object
- Estimating differential expression with DESeq2
  - Getting ready
  - How to do it...
    - Using DESeq2 from a count matrix
    - Using DESeq2 from an ExpressionSet object
  - How it works...
    - Using DESeq2 from a count matrix
    - Using DESeq2 from an ExpressionSet object
- Power analysis with powsimR
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Finding unannotated transcribed regions
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Finding regions showing high expression ab initio with bumphunter
  - Getting ready...
  - How to do it...
  - How it works...
  - There's more...
- Differential peak analysis
  - Getting ready
  - How to do it...
  - How it works...
- Estimating batch effects using SVA
  - Getting ready
  - How to do it...
  - How it works...
- Finding allele-specific expressions with AllelicImbalance
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Plotting and presenting RNAseq data
  - Getting ready
  - How to do it...
  - How it works...
Chapter 2: Finding Genetic Variants with HTS Data
- Technical requirements
- Finding SNPs and indels from sequence data using VariantTools
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
  - See also
- Predicting open reading frames in long reference sequences
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Plotting features on genetic maps with karyoploteR
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
  - See also
- Selecting and classifying variants with VariantAnnotation
  - Getting ready
  - How to do it...
  - How it works...
  - See also
- Extracting information in genomic regions of interest
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Finding phenotype and genotype associations with GWAS
  - Getting ready
  - How to do it...
  - How it works...
- Estimating the copy number at a locus of interest
  - Getting ready
  - How to do it...
  - How it works...
  - See also
Chapter 3: Searching Genes and Proteins for Domains and Motifs
- Technical requirements
- Finding DNA motifs with universalmotif
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Finding protein domains with PFAM and bio3d
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Finding InterPro domains
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
  - See also...
- Performing multiple alignments of genes or proteins
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Aligning genomic length sequences with DECIPHER
  - Getting ready
  - How to do it...
  - How it works...
- Machine learning for novel feature detection in proteins
  - Getting ready
  - How to do it...
  - How it works...
- 3D structure protein alignment with bio3d
  - Getting ready
  - How to do it...
  - How it works...
  - There's More...
Chapter 4: Phylogenetic Analysis and Visualization
- Technical requirements
- Reading and writing varied tree formats with ape and treeio
  - Getting ready
  - How to do it...
  - How it works...
  - See also
- Visualizing trees of many genes quickly with ggtree
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Quantifying differences between trees with treespace
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Extracting and working with subtrees using ape
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Creating dot plots for alignment visualization
  - Getting ready
  - How to do it...
  - How it works...
- Reconstructing trees from alignments using phangorn
  - Getting ready
  - How to do it...
  - How it works...
Chapter 5: Metagenomics
- Technical requirements
- Loading in hierarchical taxonomic data using phyloseq
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
  - See also
- Rarefying counts and correcting for sample differences using metacoder
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Reading amplicon data from raw reads with dada2
  - Getting ready
  - How to do it...
  - How it works...
  - See also
- Visualizing taxonomic abundances with heat trees in metacoder
  - Getting ready
  - How to do it...
  - How it works...
- Computing sample diversity with vegan
  - Getting ready
  - How to do it...
  - How it works...
  - See also...
- Splitting sequence files into OTUs
  - Getting ready
  - How to do it...
  - How it works...
Chapter 6: Proteomics from Spectrum to Annotation
- Technical requirements
- Representing raw MS data visually
  - Getting ready
  - How to do it...
  - How it works...
- Viewing proteomics data in a genome browser
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Visualizing distributions of peptide hit counts to find thresholds
  - Getting ready
  - How to do it...
  - How it works...
- Converting MS formats to move data between tools
  - Getting ready
  - How to do it...
  - How it works...
- Matching spectra to peptides for verification with protViz
  - Getting ready
  - How to do it...
  - How it works...
- Applying quality control filters to spectra
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Identifying genomic loci that match peptides
  - Getting ready
  - How to do it...
  - How it works...
Chapter 7: Producing Publication and Web-Ready Visualizations
- Technical requirements
- Visualizing multiple distributions with ridgeplots
  - Getting ready
  - How to do it...
  - How it works...
- Creating colormaps for two-variable data
  - Getting ready
  - How to do it...
  - How it works...
  - See also
- Representing relational data as networks
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Creating interactive web graphics with plotly
  - Getting ready
  - How to do it...
  - How it works...
- Constructing three-dimensional plots with plotly
  - Getting ready
  - How to do it...
  - How it works...
- Constructing circular genome plots of polyomic data
  - Getting ready
  - How to do it...
  - How it works...
Chapter 8: Working with Databases and Remote Data Sources
- Technical requirements
- Retrieving gene and genome annotation from BioMart
  - Getting ready
  - How to do it...
  - How it works...
- Retrieving and working with SNPs
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
  - See also
- Getting gene ontology information
  - Getting ready
  - How to do it...
  - How it works...
- Finding experiments and reads from SRA/ENA
  - Getting ready
  - How to do it...
  - How it works...
  - There's more...
- Performing quality control and filtering on high-throughput sequence reads
  - Getting ready
  - How to do it...
  - How it works...
- Completing read-to-reference alignment with external programs
  - Getting ready...
  - How to do it...
  - How it works...
- Visualizing the quality control of read-to-reference alignments
  - Getting ready...
  - How to do it...
  - How it works...
Chapter 9: Useful Statistical and Machine Learning Methods
- Technical requirements
- Correcting p-values to account for multiple hypotheses
  - Getting ready
  - How to do it...
  - How it works...
- Generating a simulated dataset to represent a background
  - Getting ready
  - How to do it...
  - How it works...
- Learning groupings within data and classifying with kNN
  - Getting ready
  - How to do it...
  - How it works...
- Predicting classes with random forests
  - Getting ready
  - How to do it...
  - How it works...
  - There's more
- Predicting classes with SVM
  - Getting ready
  - How to do it...
  - How it works...
- Learning groups in data without prior information
  - Getting ready
  - How to do it...
  - How it works...
  - There's more
- Identifying the most important variables in data with random forests
  - Getting ready
  - How to do it...
  - How it works...
- Identifying the most important variables in data with PCA
  - Getting ready
  - How to do it...
  - How it works...
Chapter 10: Programming with Tidyverse and Bioconductor
- Technical requirements
- Making base R objects tidy
  - Getting ready
  - How to do it...
  - How it works...
- Using nested dataframes
  - Getting ready
  - How it works...
  - How it works...
  - There's more...
- Writing functions for use in dplyr::mutate()
  - Getting ready
  - How to do it...
  - How it works...
- Working programmatically with Bioconductor classes
  - Getting ready
  - How to do it...
  - How it works...
- Developing reusable workflows and reports
  - Getting ready
  - How to do it...
  - How it works...
- Making use of the apply family of functions
  - Getting ready
  - How to do it...
  - How it works...
Chapter 11: Building Objects and Packages for Code Reuse
- Technical requirements
- Creating simple S3 objects to simplify code
  - Getting ready
  - How to do it...
  - How it works...
- Taking advantage of generic object functions with S3 classes
  - Getting ready
  - How to do it...
  - How it works...
- Creating structured and formal objects with the S4 system
  - Getting ready
  - How to do it...
  - How it works
  - See also
- Simple ways to package code for sharing and reuse
  - Getting ready
  - How to do it...
  - How it works...
- Using devtools to host code from GitHub
  - Getting ready
  - How to do it...
  - How it works...
- Building a unit test suite to ensure that functions work as you intend
  - Getting ready
  - How to do it...
  - How it works...
- Using continuous integration with Travis to keep code tested and up to date
  - Getting ready
  - How to do it...
  - How it works...
Other Books You May Enjoy
Index

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