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Getting ready
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Getting ready
by Dan MacLean
R Bioinformatics Cookbook
Title Page
Copyright and Credits
R Bioinformatics Cookbook
About Packt
Why subscribe?
Contributors
About the author
About the reviewer
Packt is searching for authors like you
Preface
Who this book is for
What this book covers
To get the most out of this book
Download the example code files
Download the color images
Conventions usedpacktpub.com/…/9781789950694_ColorImages.pdf
Sections
Getting ready
How to do it…
How it works…
There's more…
See also
Get in touch
Reviews
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...
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
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...
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...
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...
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...
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...
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...
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...
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...
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...
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Prev
Previous Chapter
Identifying the most important variables in data with random forests
Next
Next Chapter
How to do it...
Getting ready
We'll need the
randomForest
package and the built-in
iris
dataset.
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