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دانلود کتاب R Bioinformatics Cookbook: Utilize R packages for bioinformatics, genomics, data science, and machine learning
دانلود کتاب کتاب آشپزی بیوانفورماتیک R: از بستههای R برای بیوانفورماتیک، ژنومیک، علم داده و یادگیری ماشین استفاده کنید
مشخصات کتاب
R Bioinformatics Cookbook: Utilize R packages for bioinformatics, genomics, data science, and machine learning
ویرایش: 2
نویسندگان: Dan MacLean
سری:
ISBN (شابک) : 1837634270, 9781837634279
ناشر: Packt Publishing
سال نشر: 2023
تعداد صفحات: 396
زبان: English
فرمت فایل : PDF (درصورت درخواست کاربر به PDF، EPUB یا AZW3 تبدیل می شود)
حجم فایل: 16 مگابایت
قیمت کتاب (تومان) : 79,000
در صورت تبدیل فایل کتاب R Bioinformatics Cookbook: Utilize R packages for bioinformatics, genomics, data science, and machine learning به فرمت های PDF، EPUB، AZW3، MOBI و یا DJVU می توانید به پشتیبان اطلاع دهید تا فایل مورد نظر را تبدیل نمایند.
توجه داشته باشید کتاب کتاب آشپزی بیوانفورماتیک R: از بستههای R برای بیوانفورماتیک، ژنومیک، علم داده و یادگیری ماشین استفاده کنید نسخه زبان اصلی می باشد و کتاب ترجمه شده به فارسی نمی باشد. وبسایت اینترنشنال لایبرری ارائه دهنده کتاب های زبان اصلی می باشد و هیچ گونه کتاب ترجمه شده یا نوشته شده به فارسی را ارائه نمی دهد.
توضیحاتی درمورد کتاب به خارجی
فهرست مطالب
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 Getting ready How to do it… How it works… See also Chapter 10: Analyzing Gene Annotations Technical requirements Further information Retrieving gene and genome annotations from BioMart Getting ready How to do it… How it works… Getting Gene Ontology information for functional analysis from appropriate databases Getting ready How to do it… How it works… Using AnnoDB packages for genome annotation Getting ready How to do it… How it works… See also Using ClusterProfiler for determining GO enrichment in clusters Getting ready How to do it… How it works… Finding GO enrichment in an Ontology Conditional way with topGO Getting ready How to do it… How it works… Finding enriched KEGG pathways 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… Chapter 11: Machine Learning with mlr3 Technical requirements Further information Defining a task and learner to implement k-nearest neighbors (k-NNs) in mlr3 Getting ready How to do it… How it works… There’s more… See also... Testing the fit of the model using cross-validation Getting ready How to do it… How it works… There’s more… Using logistic regression to classify the relative likelihood of two outcomes Getting ready How to do it… How it works… See also Classifying using random forest and interpreting it with iml Getting ready How to do it… How it works… Dimension reduction with PCA in mlr3 pipelines Getting ready How to do it… How it works… There’s more… Creating a tSNE and UMAP embedding Getting ready How to do it… How it works… Clustering with k-means and hierarchical clustering Getting ready How to do it… How it works… Chapter 12: Functional Programming with purrr and base R Technical requirements Further information Making base R objects “tidy” Getting ready How to do it… How it works… Using nested dataframes for functional programming Getting ready How to do it… How it works… See also Using the apply family of functions Getting ready How to do it… How it works… Using the map family of functions in purrr Getting ready How to do it… How it works… Working with lists in purrr Getting ready How to do it… How it works… Chapter 13: Turbo-Charging Development in R with ChatGPT Technical requirements Further information Interpreting complicated code with ChatGPT assistance Getting ready How to do it… How it works… There’s more… Debugging and improving code with ChatGPT Getting ready How to do it… How it works… Generating code with ChatGPT Getting ready How to do it… How it works… There’s more… Writing documentation for R functions with ChatGPT Getting ready How to do it… How it works… There’s more… Writing unit tests for R functions with ChatGPT Getting ready How to do it… How it works… Finding R packages to build a workflow with ChatGPT Getting ready How to do it… How it works… Index Other Books You May Enjoy
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