A collection of random and not so random learning materials for computation/biology/bioinformatics. I did not screen all of the material presented here. Some might/will be inappropriate for what you want to do or learn. Please give me feedback (open a New issue) if some of the material was either useful or not. Send through more material (preferable via a pull request, clone this repo at https://github.com/sschmeier/elearningcollection) if you have any that you think are particular useful and would like to see included here. Also, some web-links that worked at the time of creating this page might not work anymore (open a New issue or sent me a correction via a pull request).

• 1. General computation/statistics/biology
• 1.1 Online courses
• 1.2 University course material
• 1.3 Other material/tutorials/books/etc.
• 2. Bioinformatics/genomics/transcriptomics/etc.
• 2.1 Online courses
• 2.2 University course material
• 2.3 Other material/tutorials/books/etc.

• Software Carpentry
• Data Carpentry
• Introduction to Linux - edX course
• Introduction to Computer Science and Programming Using Python - edX course
• Genes and the Human Condition (From Behavior to Biotechnology) - Coursera course
• Experimental Genome Science - Coursera course
• Methods in Biostatistics I - JHSPHOPEN
• Case-Based Introduction to Biostatistics - Coursera course
• Data Analysis - Coursera course
• Data Science - A Sequence of Courses: Learn to be a Data Scientist and Apply Your Skills in a Capstone Project
• The Data Scientist’s Toolbox - Coursera course
• Exploratory Data Analysis - Coursera course
• Practical Machine Learning - Coursera course
• R programming - Coursera course
• An Introduction to Interactive Programming in Python - Coursera course

• UC Davis genome center instructional videos - Instructional videos about linux and some simple bioinformatics tasks
• Stanford Open Classroom video lecture - Practical Unix
• Data Analysis and Visualization Course - UC Davis, 2012
• Unix, Perl, and Python - Course material from Bioinformatics and Research Computing at the Whitehead Institute

• Dive into Python - Free online book to learn Python programming

• A Primer on Python for Life Science Researchers
• PLoS collections, e.g.:
  • Epigenetics
• Nature Review Genetics series, e.g.:
  • Modes of transcriptional regulation
  • Regulatory elements
  • non-coding RNA
• Nature Review Molecular Cell Biology series, e.g.:
  • Post-transcriptional control
  • Stem Cells
• Nature Review Microbiology series, e.g.:
  • Systems Microbiology
  • New technologies: methods and applications

A recent article in PLoS, "A New Online Computational Biology Curriculum", by David Searls (PLoS Comput Biol 2014 10(6): e1003662. doi: 10.1371/journal.pcbi.1003662) provides a comprehensive supplementary with many programs and courses regarding bioinformatics education. Find the document here.

• Quantitative Biology Workshop - edX course
• Data Analysis for Genomics - edX course
• Bioinformatics: Life Sciences on Your Computer - Coursera course
• Bioinformatic Methods I - Coursera course
• Bioinformatic Methods II - Coursera course
• Systems Biology - A Sequence of Courses: Learn to be a Systems Biologist and Apply Your Skills in a Capstone Project

• Genomics, Bioinformatics & Medicine - Stanford University, Doug Brutlag
• Computational Molecular Biology - Stanford University, Doug Brutlag
• Introduction to Statistical and Computational Genomics - University of Washington, Borenstein-lab, 2013
• Introduction to Statistical and Computational Genomics - University of Washington, Borenstein-lab, 2014
• Genomic Informatics - University of Washington, Borenstein-lab, 2013
• Genomic Informatics - University of Washington, Borenstein-lab, 2014
• Canadian Bioinformatics Workshops material - Different courses with PDFs and VIDEOs, some examples:
  • Exploratory Analysis of Biological Data using R (2013)
  • Bioinformatics for Cancer Genomics (BiCG) (2013)
  • Informatics for RNA-sequence Analysis (2013)
  • Informatics on High Throughput Sequencing Data (2013)
• Bioinformatics and Computational Methods - Material from different courses from the Weill Medical College and Memorial Sloan-Kettering Cancer Center
• Next-Gen Sequence Analysis Workshop (2013) - Yearly workshop by Titus
• Courses focusing on different aspects of bioinformatics - UC Davis course material of past bioinformatics courses
• EBI train online - Online learning material from past courses at the European Bioinformatics Institute, e.g.
  • Next Generation Sequencing Practical Course
• Computational Biology: Genomes, Networks, Evolution - MIT video lectures
• De Novo Assembly Course - Univ. of Oslo: PDF lectures and examples free on github
• Schmeier Group bioinformatics course @ Massey University

• NCBI Handbook - Free online book explaining the tools and processes at NCBI
• WikiBooks: Next Generation Sequencing (NGS)
• A Primer of Genome Science, 3rd ed, Greg Gibson and Spencer Muse
• Bioinformatics: Sequence and Genome Analysis, Second Edition, 2nd ed, David Mount
• Essential Bioinformatics, Jin Xiong
• Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, S. Eddy, A. Krogh, G. Mitchison
• Bioinformatics: Sequence, Structure and Databanks, Des Higgins and Willie Taylor
• Bioinformatics: The Machine Learning Approach, 2nd ed, Pierre Baldi and Søren Brunak
• An Introduction to Bioinformatics Algorithms, Neil C. Jones and Pavel A. Pevzner
• Algorithms on Strings, Trees and Sequences, Dan Gusfield

• Genome speak - Speak the language of genomics
• Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
• GAGE-B: an evaluation of genome assemblers for bacterial organisms.
• GAGE: A critical evaluation of genome assemblies and assembly algorithms
• A survey of sequence alignment algorithms for next-generation sequencing
• PLoS collections, e.g.:
  • Translational Bioinformatics series
  • Computational Biology education
  • Text Mining
  • Genomics of Emerging Infectious Disease
• Nature Review Genetics series, e.g.:
  • Computational tools - Reviews on tools for analyzing genetic and genomic data
  • Modelling
  • Study design
  • Applications of next-generation sequencing
  • Genome-wide association studies
  • Translational genetics

• BioStars - An Online Question & Answer Resource for the Bioinformatics Community
• SEQanswers - the next generation sequencing community
• NCBI Education Resources - Mostly tutorials about NCBI tools and databases.
• BaRC Standard operating procedures - Standard operating procedures from Bioinformatics and Research Computing at the Whitehead Institute
• BioLinux - Linux distribution based on Ubuntu Linux that pre-installed many bioinformatics tools
• Illumina online courses - Online training videos about Illumina's sequencing technology