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A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work. The book is broken into three parts: Introduction to Unix/Linux: The command-line is the “natural environment” of scientific computing, and this part covers a wide range of topics, including logging in, working with files and directories, installing programs and writing scripts, and the powerful “pipe” operator for file and data manipulation. Programming in Python: Python is both a premier language for learning and a common choice in scientific software development. This part covers the basic concepts in programming (data types, if-statements and loops, functions) via examples of DNA-sequence analysis. This part also covers more complex subjects in software development such as objects and classes, modules, and APIs. Programming in R: The R language specializes in statistical data analysis, and is also quite useful for visualizing large datasets. This third part covers the basics of R as a programming language (data types, if-statements, functions, loops and when to use them) as well as techniques for large-scale, multi-test analyses. Other topics include S3 classes and data visualization with ggplot2.
- Subjects:
- Biology
- Keywords:
- Computational biology Textbooks
- Resource Type:
- e-book
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e-book
This is a new approach to an introductory statistical inference textbook, motivated by probability theory as logic. It is targeted to the typical Statistics 101 college student, and covers the topics typically covered in the first semester of such a course. It is freely available under the Creative Commons License, and includes a software library in Python for making some of the calculations and visualizations easier.
- Subjects:
- Mathematics and Statistics
- Keywords:
- Mathematical statistics Textbooks
- Resource Type:
- e-book
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e-book
Think Bayes is an introduction to Bayesian statistics using computational methods. The premise of this book, and the other books in the Think X series, is that if you know how to program, you can use that skill to learn other topics. Most books on Bayesian statistics use mathematical notation and present ideas in terms of mathematical concepts like calculus. This book uses Python code instead of math, and discrete approximations instead of continuous mathematics. As a result, what would be an integral in a math book becomes a summation, and most operations on probability distributions are simple loops. I think this presentation is easier to understand, at least for people with programming skills. It is also more general, because when we make modeling decisions, we can choose the most appropriate model without worrying too much about whether the model lends itself to conventional analysis. Also, it provides a smooth development path from simple examples to real-world problems.
- Subjects:
- Computing and Mathematics and Statistics
- Keywords:
- Bayesian statistical decision theory Python (Computer program language) Textbooks
- Resource Type:
- e-book
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e-book
Think Stats is an introduction to Probability and Statistics for Python programmers. Think Stats emphasizes simple techniques you can use to explore real data sets and answer interesting questions. The book presents a case study using data from the National Institutes of Health. Readers are encouraged to work on a project with real datasets. If you have basic skills in Python, you can use them to learn concepts in probability and statistics. Think Stats is based on a Python library for probability distributions (PMFs and CDFs). Many of the exercises use short programs to run experiments and help readers develop understanding.
- Subjects:
- Computing and Mathematics and Statistics
- Keywords:
- Textbooks Statistics -- Computer programs
- Resource Type:
- e-book