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 Authors
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 45-day 100% Happiness Guarantee
Within 45 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$11,038,020writing, 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
Retrocomputing with Clash
Gergő ÉrdiHaskell for FPGA Hardware Design: Use abstractions like monads and lenses to implement 1970's retro-computing devices like arcade machines and home computers.
- #2
Aprendiendo Git
Miguel Angel Durán GarcíaGit no es complicado... ¡Si lo entiendes! 😜
¿Sientes que sabes usarlo porque has memorizado todos los comandos que necesitas? ¡Pero no entiendes qué hace cada cosa y por qué! Así es normal que, cuando exista un problema, te cueste resolverlo.
¡Con este libro vas a entender de una vez por todas todo lo que es Git y cómo sacarle provecho!
- #3
C++ Best Practices
Jason TurnerLevel up your C++, get the tools working for you, eliminate common problems, and move on to more exciting things!
- #4
Stratospheric
Tom Hombergs, Björn Wilmsmann, and Philip RiecksFrom Zero to Production with Spring Boot and AWS. All you need to know to get a Spring Boot application into production with AWS. No previous AWS knowledge required.
Go to stratospheric.dev for a tour of the contents.
- #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
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.
- #7
Atomic Kotlin
Bruce Eckel and Svetlana IsakovaFor both beginning and experienced programmers! From the author of the multi-award-winning Thinking in C++ and Thinking in Java and a Kotlin team member comes a book that breaks concepts into small, easy-to-digest "atoms," along with exercises supported by hints and solutions directly inside IntelliJ IDEA! Full support at www.AtomicKotlin.com.
- #8
Cloud Strategy
Gregor Hohpe“Strategy is the difference between making a wish and making it come true.” A successful migration to the cloud can transform your organization, but it shouldn’t be driven by wishes. This book tells you how to develop a sound strategy guided by frameworks and decision models without being overly abstract nor getting lost in product details.
- #9
Introducing EventStorming
Alberto BrandoliniThe deepest tutorial and explanation about EventStorming, straight from the inventor.
- #10
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.
Top Bundles
- #1
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... - #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
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!? - #5
Retromat eBook Bundle for Agile Retrospectives
2 Books
If you facilitate retrospectives this bundle is for you: "Plans for Retrospectives" helps beginners learn the lay of the land with tried-and-true plans. Once you know your way around, "Run great agile retrospectives" contains all 135+ activities in Retromat for you to mix and match. - #6
Books on problem-solving using Agile, Lean, Complexity, and more
6 Books
Six great books on problem-solving. Learn how to deal with impediments using agile practices, do A3 problem-solving with lean thinking, apply complexity science, finding root causes, and do event storming. All in one buy for a largely reduced price! Books included Agile teams need to be able to handle impediments. The book Problem? What Problem?... - #7
10 Books Bundle - A New Career in Tech 🚀
10 Books
Do you want to create yourself a new and profitable skillset - in one year or less? Do you want to position yourself on the right side of change finally? Do you want to work from home and set your own work schedule while choosing fun and interesting coding projects? Software developers and freelance developersearn six figuresin the US, according... - #9
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... - #10
Accelerated Windows Memory Dump Analysis
2 Books
The full-color transcript of Software Diagnostics Services training sessions with 32 step-by-step exercises, notes, source code of specially created modeling applications, and more than 100 questions and answers. Covers more than 65 crash dump analysis patterns from x86 and x64 process, kernel, and complete (physical) memory dumps. Learn how to...
