Data Analysis for the Life Sciences
Data Analysis for the Life Sciences
About the Book
The unprecedented advance in digital technology during the second half of the 20th century has produced a measurement revolution that is transforming science. In the life sciences, data analysis is now part of practically every research project. Genomics, in particular, is being driven by new measurement technologies that permit us to observe certain molecular entities for the first time. These observations are leading to discoveries analogous to identifying microorganisms and other breakthroughs permitted by the invention of the microscope. Choice examples of these technologies are microarrays and next generation sequencing. This book will cover several of the statistical concepts and data analytic skills needed to succeed in data-driven life science research. We go from relatively basic concepts related to computing p-values to advanced topics related to analyzing high-throughput data.
While statistics textbooks focus on mathematics, this book focuses on using a computer to perform data analysis. Instead of explaining the mathematics and theory, and then showing examples, we start by stating a practical data-related challenge. This book also includes the computer code that provides a solution to the problem and helps illustrate the concepts behind the solution. By running the code yourself, and seeing data generation and analysis happen live, you will get a better intuition for the concepts, the mathematics, and the theory. The book was created using the R markdown language and we make all this code available to the reader. This means that readers can replicate all the figures and analyses used to create the book.
About the Contributors
Table of Contents
- Acknowledgements
-
Introduction
- What Does This Book Cover?
- How Is This Book Different?
-
Getting Started
- Installing R
- Installing RStudio
- Learn R Basics
- Installing Packages
- Importing Data into R
-
Brief Introduction to
dplyr - Mathematical Notation
-
Inference
- Introduction
- Random Variables
- The Null Hypothesis
- Distributions
- Probability Distribution
- Normal Distribution
- Populations, Samples and Estimates
- Central Limit Theorem and t-distribution
- Central Limit Theorem in Practice
- t-tests in Practice
- The t-distribution in Practice
- Confidence Intervals
- Power Calculations
- Monte Carlo Simulation
- Parametric Simulations for the Observations
- Permutation Tests
- Association Tests
-
Exploratory Data Analysis
- Quantile Quantile Plots
- Boxplots
- Scatterplots And Correlation
- Stratification
- Bi-variate Normal Distribution
- Plots To Avoid
- Misunderstanding Correlation (Advanced)
- Robust Summaries
- Wilcoxon Rank Sum Test
-
Matrix Algebra
- Motivating Examples
- Matrix Notation
- Solving System of Equations
- Vectors, Matrices and Scalars
- Matrix Operations
- Examples
-
Linear Models
- The Design Matrix
- The Mathematics Behind lm()
- Standard Errors
- Interactions and Contrasts
- Linear Model with Interactions
- Analysis of variance
- Co-linearity
- Rank
- Removing Confounding
- The QR Factorization (Advanced)
- Going Further
-
Inference For High Dimensional Data
- Introduction
- Inference in Practice
- Procedures
- Error Rates
- The Bonferroni Correction
- False Discovery Rate
- Direct Approach to FDR and q-values (Advanced)
- Basic Exploratory Data Analysis
-
Statistical Models
- The Binomial Distribution
- The Poisson Distribution
- Maximum Likelihood Estimation
- Distributions for Positive Continuous Values
- Bayesian Statistics
- Hierarchical Models
-
Distance and Dimension Reduction
- Introduction
- Euclidean Distance
- Distance in High Dimensions
- Dimension Reduction Motivation
- Singular Value Decomposition
- Projections
- Rotations
- Multi-Dimensional Scaling Plots
- Principal Component Analysis
-
Basic Machine Learning
- Clustering
- Conditional Probabilities and Expectations
- Smoothing
- Bin Smoothing
- Loess
- Class Prediction
- Cross-validation
-
Batch Effects
- Confounding
- Confounding: High-throughput Example
- Discovering Batch Effects with EDA
- Gene Expression Data
- Motivation for Statistical Approaches
- Adjusting for Batch Effects with Linear Models
- Factor Analysis
- Modeling Batch Effects with Factor Analysis
The Leanpub 60-day 100% Happiness Guarantee
Within 60 days of purchase you can get a 100% refund on any Leanpub purchase, in two clicks.
See full terms
Do Well. Do Good.
Authors have earned$11,592,641writing, publishing and selling on Leanpub, earning 80% royalties while saving up to 25 million pounds of CO2 and up to 46,000 trees.
Learn more about writing on Leanpub
Free Updates. DRM Free.
If you buy a Leanpub book, you get free updates for as long as the author updates the book! Many authors use Leanpub to publish their books in-progress, while they are writing them. All readers get free updates, regardless of when they bought the book or how much they paid (including free).
Most Leanpub books are available in PDF (for computers), EPUB (for phones and tablets) and MOBI (for Kindle). The formats that a book includes are shown at the top right corner of this page.
Finally, Leanpub books don't have any DRM copy-protection nonsense, so you can easily read them on any supported device.
Learn more about Leanpub's ebook formats and where to read them
Top Books
- #1
SignalR on .NET 6 - the Complete Guide
Fiodar SazanavetsLearn everything there is to learn about SignalR and how to integrate it with the latest .NET 6 and C# 10 features. Learn how to connect any type of client to SignalR, including plain WebSocket client. Learn how to build interactive applications that can communicate with each other in real time without making excessive calls.
- #2
The easiest way to learn design patterns
Fiodar SazanavetsLearn design patterns in the easiest way possible. You will no longer have to brute-force your way through each one of them while trying to figure out how it works. The book provides a unique methodology that will make your understanding of design patterns stick. It can also be used as a reference book where you can find design patterns in seconds.
- #3
C++20 - The Complete Guide
Nicolai M. JosuttisAll the new language and library features of C++20 (for those who know previous versions).
The book presents all new language and library features of C++20. Learn how this impacts day-to-day programming, to benefit in practice, to combine new features, and to avoid all new traps.
Buy early, pay less, free updates.
Other books:
- #4
Jetpack Compose internals
Jorge CastilloJetpack Compose is the future of Android UI. Master how it works internally and become a more efficient developer with it. You'll also find it valuable if you are not an Android dev. This book provides all the details to understand how the Compose compiler & runtime work, and how to create a client library using them.
- #5
Functional event-driven architecture: Powered by Scala 3
Gabriel VolpeExplore the event-driven architecture (EDA) in a purely functional way, mainly powered by Fs2 streams in Scala 3!
Leverage your functional programming skills by designing and writing stateless microservices that scale, powered by stateful message brokers.
- #6
OpenIntro Statistics
David Diez, Christopher Barr, Mine Cetinkaya-Rundel, and OpenIntroA complete foundation for Statistics, also serving as a foundation for Data Science.
Leanpub revenue supports OpenIntro (US-based nonprofit) so we can provide free desk copies to teachers interested in using OpenIntro Statistics in the classroom and expand the project to support free textbooks in other subjects.
More resources: openintro.org.
- #7
R Programming for Data Science
Roger D. PengThis book brings the fundamentals of R programming to you, using the same material developed as part of the industry-leading Johns Hopkins Data Science Specialization. The skills taught in this book will lay the foundation for you to begin your journey learning data science. Printed copies of this book are available through Lulu.
- #8
Ansible for DevOps
Jeff GeerlingAnsible is a simple, but powerful, server and configuration management tool. Learn to use Ansible effectively, whether you manage one server—or thousands.
- #9
CCIE Service Provider Version 4 Written and Lab Exam Comprehensive Guide
Nicholas RussoThe service provider landscape has changed rapidly over the past several years. Networking vendors are continuing to propose new standards, techniques, and procedures for overcoming new challenges while concurrently reducing costs and delivering new services. Cisco has recently updated the CCIE Service Provider track to reflect these changes; this book represents the author's personal journey in achieving that certification.
- #10
Cronache di Domain-Driven Design
Francesco Strazzullo, Matteo Baglini, Gianluca Padovani, Emanuele DelBono, Marco Consolaro, Alessandro Colla, Uberto Barbini, Alberto Acerbis, Julie Camosseto, DDD Open, and Alberto BrandoliniCronache di Domain-Driven Design: un libro corale in italiano fatto di storie indipendenti tra loro, che sono il risultato dell’applicazione di Domain-Driven Design su progetti reali.
Top Bundles
- #1
Practical FP in Scala + Functional event-driven architecture
2 Books
Practical FP in Scala (A hands-on approach) & Functional event-driven architecture, aka FEDA, (Powered by Scala 3), together as a bundle! The content of PFP in Scala is a requirement to understand FEDA so why not take advantage of this bundle!? - #2
Software Architecture for Developers: Volumes 1 & 2 - Technical leadership and communication
2 Books
"Software Architecture for Developers" is a practical and pragmatic guide to modern, lightweight software architecture, specifically aimed at developers. You'll learn:The essence of software architecture.Why the software architecture role should include coding, coaching and collaboration.The things that you really need to think about before... - #3
All the Books of The Medical Futurist
6 Books
We put together the most popular books from The Medical Futurist to provide a clear picture about the major trends shaping the future of medicine and healthcare. Digital health technologies, artificial intelligence, the future of 20 medical specialties, big pharma, data privacy, digital health investments and how technology giants such as Amazon... - #4
CCIE Service Provider Ultimate Study Bundle
2 Books
Piotr Jablonski, Lukasz Bromirski, and Nick Russo have joined forces to deliver the only CCIE Service Provider training resource you'll ever need. This bundle contains a detailed and challenging collection of workbook labs, plus an extensively detailed technical reference guide. All of us have earned the CCIE Service Provider certification... - #6
Pattern-Oriented Memory Forensics and Malware Detection
2 Books
This training bundle for security engineers and researchers, malware and memory forensics analysts includes two accelerated training courses for Windows memory dump analysis using WinDbg. It is also useful for technical support and escalation engineers who analyze memory dumps from complex software environments and need to check for possible... - #7
Modern C++ Collection
3 Books
Get All about Modern C++C++ Standard Library, including C++20Concurrency with Modern C++, including C++20C++20Each book has about 200 complete code examples. Updates are included. When I update one of the books, you immediately get the updated bundle. You can expect significant updates to each new C++ standard (C++23, C++26, .. ) and also... - #10
Growing Agile: The Complete Coach's Guide
7 Books
Growing Agile: Coach's Guide Series This bundle provides a collection of training and workshop plans for a variety of agile topics. The series is aimed at agile coaches, trainers and ScrumMasters who often find themselves needing to help teams understand agile concepts. Each book in the series provides the plans, slides, handouts and activity...
