R Bioinformatics Cookbook Utilize R Packages for Bioinformatics, Genomics, Data Science, and Machine Learning
The updated second edition of R Bioinformatics Cookbook takes a recipe-based approach to show you how to conduct practical research and analysis in computational biology with R. You’ll learn how to create a useful and modular R working environment, along with loading, cleaning, and analyzing data us...
| Other Authors: | |
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| Format: | eBook |
| Language: | Inglés |
| Published: |
Birmingham, England :
Packt Publishing Ltd
[2023]
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| Edition: | Second edition |
| Subjects: | |
| See on Biblioteca Universitat Ramon Llull: | https://discovery.url.edu/permalink/34CSUC_URL/1im36ta/alma991009781236906719 |
Table of Contents:
- Cover
- Title Page
- Copyright and Credits
- Dedications
- Contributors
- Table of Contents
- Preface
- Chapter 1: Setting Up Your R Bioinformatics Working Environment
- Technical requirements
- Further information
- Setting up an R project in a directory
- Getting ready
- How to do it…
- How it works…
- There's more…
- Using the here package to simplify working with paths
- Getting ready
- How to do it…
- How it works…
- There's more…
- Using the devtools package to work with the latest non-CRAN packages
- Getting ready
- How to do it…
- How it works…
- There's more…
- Setting up your machine for the compilation of source packages
- Getting ready
- How to do it…
- How it works…
- See also
- Using the renv package to create a project-specific set of packages
- Getting ready
- How to do it…
- How it works…
- There's more…
- Installing and managing different versions of Bioconductor packages in environments
- Getting ready
- How to do it…
- How it works…
- Using bioconda to install external tools
- swGetting ready
- How to do it…
- How it works…
- Chapter 2: Loading, Tidying, and Cleaning Data in the tidyverse
- Technical requirements
- Further information
- Loading data from files with readr
- Getting ready
- How to do it…
- How it works…
- There's more…
- See also
- Tidying a wide format table into a tidy table with tidyr
- Getting ready
- How to do it…
- How it works…
- See also
- Tidying a long format table into a tidy table with tidyr
- Getting ready
- How it works…
- There's more…
- Combining tables using join functions
- Getting ready
- How to do it…
- How it works…
- Reformatting and extracting existing data into new columns using stringr
- Getting ready
- How to do it…
- How it works….
- Computing new data columns from existing ones and applying arbitrary functions using mutate()
- Getting ready
- How to do it…
- How it works…
- Using dplyr to summarize data in large tables
- Getting ready
- How to do it…
- How it works…
- Using datapasta to create R objects from cut-and-paste data
- Getting ready
- How to do it…
- How it works…
- There's more…
- Chapter 3: ggplot2 and Extensions for Publication Quality Plots
- Technical requirements
- Further information
- Combining many plot types in ggplot2
- Getting ready
- How to do it…
- How it works…
- There's more…
- Comparing changes in distributions with ggridges
- Getting ready
- How to do it…
- How it works…
- Customizing plots with ggeasy
- Getting ready
- How to do it…
- How it works…
- There's more…
- Highlighting selected values in busy plots with gghighlight
- Getting ready
- How to do it…
- How it works…
- Plotting variability and confidence intervals better with ggdist
- Getting ready
- How to do it…
- How it works…
- Making interactive plots with plotly
- Getting ready
- How to do it…
- How it works…
- See also
- Clarifying label placement with ggrepel
- Getting ready
- How to do it…
- How it works…
- Zooming and making callouts from selected plot sections with facetzoom
- Getting ready
- How to do it…
- How it works…
- Getting ready
- How to do it…
- How it works…
- There's more…
- See also
- Chapter 4: Using Quarto to Make Data-Rich Reports, Presentations, and Websites
- Technical requirements
- Further information
- Using Markdown and Quarto for literate computation
- Getting ready
- How to do it…
- How it works…
- There's more…
- Creating different document formats from the same source
- Getting ready
- How to do it…
- How it works…
- Creating data-rich presentations from code
- Getting ready.
- How to do it…
- How it works…
- There's more…
- Creating websites from collections of Quarto documents
- Getting ready
- How to do it…
- How it works…
- There's more…
- See also
- Adding interactivity with Shiny
- Getting ready
- How to do it…
- How it works…
- There's more…
- See also
- Chapter 5: Easily Performing Statistical Tests Using Linear Models
- Technical requirements
- Further information
- Modeling data with a linear model
- Getting ready
- How to do it…
- How it works…
- There's more…
- Using a linear model to compare the mean of two groups
- Getting ready
- How to do it…
- How it works…
- There's more…
- Using a linear model and ANOVA to compare multiple groups in a single variable
- Getting ready
- How to do it…
- How it works…
- There's more…
- Using linear models and ANOVA to compare multiple groups in multiple variables
- Getting ready
- How to do it…
- How it works…
- Testing and accounting for interactions between variables in linear models
- Getting ready
- How to do it…
- How it works…
- Doing tests for differences in data in two categorical variables
- Getting ready
- How to do it…
- How it works…
- Making predictions using linear models
- Getting ready
- How to do it…
- How it works…
- See also
- Chapter 6: Performing Quantitative RNA-seq
- Technical requirements
- Further information
- Estimating differential expression with edgeR
- Getting ready
- How to do it…
- How it works…
- Estimating differential expression with DESeq2
- Getting ready
- How to do it…
- How it works…
- There's more...
- Estimating differential expression with Kallisto and Sleuth
- Getting ready
- How to do it…
- How it works…
- Using Sleuth to analyze time course experiments
- Getting ready
- How to do it…
- How it works…
- Analyzing splice variants with SGSeq
- Getting ready.
- How to do it…
- How it works…
- Performing 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 using 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 with SVA
- Getting ready
- How to do it…
- How it works…
- Finding allele-specific expression with AllelicImbalance
- Getting ready
- How to do it…
- How it works…
- There's more…
- Presenting RNA-Seq data using ComplexHeatmap
- Getting ready
- How to do it…
- How it works…
- Chapter 7: Finding Genetic Variants with HTS Data
- Technical requirements
- Further information
- 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 8: Searching Gene and Protein Sequences for Domains and Motifs
- Technical requirements.
- Further information
- 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…
- Finding transmembrane domains with tmhmm and pureseqTM
- Getting ready
- How to do it…
- How it works…
- There's more…
- See also
- Creating figures of protein domains using drawProteins
- Getting ready
- How to do it…
- How it works…
- There's more…
- Performing multiple alignments of proteins or genes
- 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…
- Novel feature detection in proteins
- Getting ready
- How to do it…
- How it works…
- 3D structure protein alignment in bio3d
- Getting ready
- How to do it…
- How it works…
- There's more…
- Chapter 9: Phylogenetic Analysis and Visualization
- Technical requirements
- Further information
- 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 and estimating the 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 visualizations
- Getting ready
- How to do it…
- How it works…
- Reconstructing trees from alignments using phangorn
- Getting ready
- How to do it…
- How it works….
- Finding orthologue candidates using reciprocal BLASTs.
