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
Authors have earned$9,886,858writing, 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
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
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
C++ Best Practices
Jason TurnerLevel up your C++, get the tools working for you, eliminate common problems, and move on to more exciting things!
- #2
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.
- #3
Functional Design and Architecture
Alexander GraninSoftware Design in Functional Programming, Design Patterns and Practices, Methodologies and Application Architectures. How to build real software in Haskell with less efforts and low risks. The first complete source of knowledge.
- #4
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 together with a member of the Kotlin language team comes a book that breaks the concepts into small, easy-to-digest "atoms," along with exercises supported by hints and solutions directly inside IntelliJ IDEA!
- #5
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.
- #6
I am a Software Engineer and I am in Charge
Alexis Monville and Michael DoyleI am a Software Engineer and I am in Charge is a real-world, practical book that helps you increase your impact and satisfaction at work no matter who you work with.
In the book, we will follow Sandrine, a fictional character who learns to think in a new way enabling her to take a different course of action.
- #7
C++20
Rainer GrimmC++20 is the next big C++ standard after C++11. As C++11 did it, C++20 changes the way we program modern C++. This change is, in particular, due to the big four of C++20: ranges, coroutines, concepts, and modules.
- #8
Invest In Digital Health - The Medical Futurist's Guide
Dr. Bertalan MeskoArtificial Intelligence and Digital Health are booming. In this book, we explain why now it's a good time to invest in Digital Health and give recommendations on where to invest by looking at the top 24 technological trends we find the most promising.
- #9
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.
- #10
The Hundred-Page Machine Learning Book
Andriy BurkovEverything you really need to know in Machine Learning in a hundred pages.
Top Bundles
- #1
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... - #2
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... - #3
The Future of Digital Health
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 and how technology giants such as Amazon or Google want to conquer... - #4
Cisco CCNA 200-301 Complet
4 Books
Ce lot comprend les quatre volumes du guide préparation à l'examen de certification Cisco CCNA 200-301. - #5
Modern Management Made Easy
3 Books
Read all three Modern Management Made Easy books. Learn to manage yourself, lead and serve others, and lead the organization. - #6
CCDE Practical Studies (All labs)
3 Books
CCDE lab - #7
Modern C++ by Nicolai Josuttis
2 Books
- #8
"The C++ Standard Library" and "Concurrency with Modern C++"
2 Books
Get my books "The C++ Standard Library" and "Concurrency with Modern C++" in a bundle. The first book gives you the details you should know about the C++ standard library; the second one dives deeper into concurrency with modern C++. In sum, you get more than 600 pages full of modern C++ and about 250 source files presenting the standard library... - #9
Linux Administration Complet
4 Books
Ce lot comprend les quatre volumes du Guide Linux Administration :Linux Administration, Volume 1, Administration fondamentale : Guide pratique de préparation aux examens de certification LPIC 1, Linux Essentials, RHCSA et LFCS. Administration fondamentale. Introduction à Linux. Le Shell. Traitement du texte. Arborescence de fichiers. Sécurité... - #10
Advanced Product Management
3 Books
Get The Art of Strategy, Product Discovery and Lean Product Management with a 20% discount.
