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9 materials found

Authors: Aidan Budd  or András Aszódi 


Statistics with R

The aim of this course is to teach you how to perform basic statistical analysis using R. First we review the foundations (sampling theory, discrete and continuous distributions), then we focus on classical hypothesis testing. This course will improve your generic statistics knowledge....

Scientific topics: Statistics and probability

Keywords: Biostatistics, R

Python programming primer

The purpose of this training is to teach general programming concepts using Python as an instruction tool.
Topics:
Introduction to Python: basic principles.
Python data structures: strings, tuples, lists, dictionaries, sets.
Object-oriented programming: how to model coffee machines in Python...

Scientific topics: Software engineering

Keywords: Python biologists

R as a programming language

This course is aimed at colleagues who would like to learn how to use the statistical programming language "R". We will learn about the data structures and functions in R, and how to write R scripts.
Topics:
Introduction to R: general principles.
Data structures in R: vectors, matrices, arrays,...

Keywords: R programming

UNIX command line and scripting

The first part of this course introduces the UNIX command line on a Linux or Mac. The second part provides a basic introduction to string searches and scripting with AWK and BASH.

Keywords: Awk, Bash, Unix

Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies

Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.

Keywords: Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment

Summarising sets of phylogenies

A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes...

Keywords: Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics

Introduction to Multiple Sequence Alignment

An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of...

Keywords: Multiple sequence analysis, Protein structure, Sequence analysis

Introduction to Bioinformatics

An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could...

Keywords: Introduction bioinformatics

Interpreting Phylogenies

Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday.
Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic...

Keywords: Molecular evolution, Phylogenetics