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Keywords: Experimental-design  or Babraham Institute  or Programming 


Bioinformática con Ñ

"Bioinformática con Ñ" is a project born in 2013 aimed to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The first release, published in 2014 and edited by Álvaro Sebastián and Alberto Pascual-García, consists on more than 500 pages where the following...

Scientific topics: Systems biology, Bioinformatics

Keywords: introduction to bioinformatics, structural biology, biomolecular databases, Systems biology, phylogenetics, Programming, Sequence Analysis, DNA RNA, Virtual Screening, molecular evolution, molecular dynamics, Molecular docking, normal modes analysis, Proteins, protein folding, protein structure alignment, chromatin structure, intrinsically disordered proteins, data minning, R-programming, parallel computing, bibliography management

Resource type: Book

Bioinformática con Ñ https://tess.elixir-europe.org/materials/bioinformatica-con-n "Bioinformática con Ñ" is a project born in 2013 aimed to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The first release, published in 2014 and edited by Álvaro Sebastián and Alberto Pascual-García, consists on more than 500 pages where the following matters are covered: biomedical databases, sequence analysis, phylogeny and evolution, structural biology, including diverse topics such as docking, virtual screening or molecular dynamics, statistics and R, systems biology, programming skills, data mining, parallel computation, bibliography management and science article writing. Portada: Enrique Sahagún Systems biology Bioinformatics introduction to bioinformatics, structural biology, biomolecular databases, Systems biology, phylogenetics, Programming, Sequence Analysis, DNA RNA, Virtual Screening, molecular evolution, molecular dynamics, Molecular docking, normal modes analysis, Proteins, protein folding, protein structure alignment, chromatin structure, intrinsically disordered proteins, data minning, R-programming, parallel computing, bibliography management Anyone interested in bioinformatics
Quality Control in Sequencing Experiments

This course looks at the different ways in which sequencing based studies can fail and the options for visualisation and QC which allow you to identify and diagnose these failures at an early stage. It is designed to be of use to anyone who is using sequencing as part of their research, not just...

Scientific topics: Quality affairs

Keywords: Babraham Institute

Quality Control in Sequencing Experiments https://tess.elixir-europe.org/materials/quality-control-in-sequencing-experiments This course looks at the different ways in which sequencing based studies can fail and the options for visualisation and QC which allow you to identify and diagnose these failures at an early stage. It is designed to be of use to anyone who is using sequencing as part of their research, not just those who are running sequencing facilities. Quality affairs Babraham Institute
Extracting biological information from gene lists

Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting...

Keywords: Functional analysis, Gene lists, Babraham Institute

Extracting biological information from gene lists https://tess.elixir-europe.org/materials/extracting-biological-information-from-gene-lists Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists. This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication. Functional analysis, Gene lists, Babraham Institute
Sample size estimation

Power analysis is a method to estimate the samples sizes needed to detect statistical effects with high probability. This course provides an introduction to the basic principles of power analysis and goes through the variables for power calculation. It also addresses the issues associated with...

Keywords: Power analysis, Sample size, Babraham Institute

Sample size estimation https://tess.elixir-europe.org/materials/sample-size-estimation Power analysis is a method to estimate the samples sizes needed to detect statistical effects with high probability. This course provides an introduction to the basic principles of power analysis and goes through the variables for power calculation. It also addresses the issues associated with technical and biological replicates. The program is intended for people who have no prior knowledge of power. Basic statistical knowledge is extremely useful but prior attendance on a statistics course is not compulsary. Power analysis, Sample size, Babraham Institute
Statistical Analysis using SPSS

Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package.

Scientific topics: Statistics and probability

Keywords: Babraham Institute

Statistical Analysis using SPSS https://tess.elixir-europe.org/materials/statistical-analysis-using-spss Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package. Statistics and probability Babraham Institute
Statistical Analysis using GraphPad Prism

GraphPad Prism is a powerful and friendly package which allows you to plot and analyse your data. This course acts not only as an introduction to Prism, but also goes through the basic statistical knowledge which should allow you to make the most of your data.

Keywords: GraphPad Prism, Babraham Institute

Statistical Analysis using GraphPad Prism https://tess.elixir-europe.org/materials/statistical-analysis-using-graphpad-prism GraphPad Prism is a powerful and friendly package which allows you to plot and analyse your data. This course acts not only as an introduction to Prism, but also goes through the basic statistical knowledge which should allow you to make the most of your data. GraphPad Prism, Babraham Institute
Scientific Figure Design

This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and...

Scientific topics: Data visualisation

Keywords: Figure design, Babraham Institute

Scientific Figure Design https://tess.elixir-europe.org/materials/scientific-figure-design This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures. The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools. Data visualisation Figure design, Babraham Institute
An Introduction to Unix

Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this. This course provides an introduction to the concepts of unix and provides a...

Keywords: Unix, Babraham Institute

An Introduction to Unix https://tess.elixir-europe.org/materials/an-introduction-to-unix Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this. This course provides an introduction to the concepts of unix and provides a practical introduction to working in this environment. Internally we link this course to a more specific course illustrating the use of our internal cluster environment and this part of the course could be adapted for other sites with different compute infrastructure. Unix, Babraham Institute
An Introduction to ggplot

Ggplot is the most popular plotting extension to R and replicates many of the graph types found in the core plotting libraries. This course provides an introduction to the ggplot2 libraries and gives a practical guide for how to use these to create different types of graphs.

Keywords: ggPlot, Babraham Institute

An Introduction to ggplot https://tess.elixir-europe.org/materials/an-introduction-to-ggplot Ggplot is the most popular plotting extension to R and replicates many of the graph types found in the core plotting libraries. This course provides an introduction to the ggplot2 libraries and gives a practical guide for how to use these to create different types of graphs. ggPlot, Babraham Institute
Plotting complex figures with R

This course is a comprehensive guide to the use of the built in R plotting functionality to construct everything from customised simple plots to complex multi-layered figures. It follows on from the material in our introductory R course and participants are expected to have a basic understanding...

Keywords: Graph plotting, R Programming, Babraham Institute

Plotting complex figures with R https://tess.elixir-europe.org/materials/plotting-complex-figures-with-r This course is a comprehensive guide to the use of the built in R plotting functionality to construct everything from customised simple plots to complex multi-layered figures. It follows on from the material in our introductory R course and participants are expected to have a basic understanding of R - enough to load and do basic manipulation of datasets. Graph plotting, R Programming, Babraham Institute
Advanced R

This course follows on from the introductory course. It goes into more detail on practical guides to filtering and combining complex data sets. It also looks at other core R concepts such as looping with apply statements and using packages. Finally it looks at how to document your R analyses and...

Keywords: R programming, Babraham Institute

Advanced R https://tess.elixir-europe.org/materials/advanced-r This course follows on from the introductory course. It goes into more detail on practical guides to filtering and combining complex data sets. It also looks at other core R concepts such as looping with apply statements and using packages. Finally it looks at how to document your R analyses and generate complete analysis reports. R programming, Babraham Institute
Introduction to R

R is a popular language and environment that allows powerful and fast manipulation of data, offering many statistical and graphical options. This course aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. It will focus...

Scientific topics: Software engineering

Keywords: R programming, Babraham Institute

Introduction to R https://tess.elixir-europe.org/materials/introduction-to-r R is a popular language and environment that allows powerful and fast manipulation of data, offering many statistical and graphical options. This course aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. It will focus on entering and manipulating data in R and producing simple graphs. A few functions for basic statistics will be briefly introduced, but statistical functions will not be covered in detail. Software engineering R programming, Babraham Institute
Learning to Program with Perl

This course aims to introduce the basic features of the Perl language. At the end you should have everything you need to write moderately complicated programs, and enough pointers to other resources to get you started on bigger projects. The course tries to provide a grounding in the basic theory...

Keywords: perl, Babraham Institute

Learning to Program with Perl https://tess.elixir-europe.org/materials/learning-to-program-with-perl This course aims to introduce the basic features of the Perl language. At the end you should have everything you need to write moderately complicated programs, and enough pointers to other resources to get you started on bigger projects. The course tries to provide a grounding in the basic theory you'll need to write programs in any language as well as an appreciation for the right way to do things in Perl. perl, Babraham Institute
Analysing Mapped Sequence Data with SeqMonk

SeqMonk is a program which can analyse large data sets of mapped genomic positions. It is most commonly used to work with data coming from high-throughput sequencing pipelines. The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let...

Scientific topics: Sequence alignment

Keywords: Babraham Institute

Analysing Mapped Sequence Data with SeqMonk https://tess.elixir-europe.org/materials/analysing-mapped-sequence-data-with-seqmonk SeqMonk is a program which can analyse large data sets of mapped genomic positions. It is most commonly used to work with data coming from high-throughput sequencing pipelines. The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let you identify regions of interest. It is a friendly way to explore and analysis very large datasets. This course provides an introduction to the main features of SeqMonk and will run through the anlaysis of a couple of different datasets to show what sort of analysis options it provides. Sequence alignment Babraham Institute
UNIX Fundamentals

This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. At the end of...

Keywords: Problem based learning, Programming, Unix

UNIX Fundamentals https://tess.elixir-europe.org/materials/unix-fundamentals-35adf82d-ae32-449d-9627-43b5d18da8cc This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. At the end of the course, participants are expected to be able to: Have some understanding on UNIX systems Navigate through the UNIX filesystem Execute and understand some UNIX process commands Correctly set file permissions Perform basic file management Participants are encouraged to follow the tutorial sections sequentially. The tutorial content is sometimes an oversimplification of the Truth - yes, we know! Due to the diversity of computer systems, we will just assume that participants do have access to a terminal. For help, please contact your IT support - or a good friend!Authors are affiliated to the SIB Swiss Institute of Bioinformatics: Vassilios IoannidisWith some content provided by Frédéric Schütz, Volker Flegel and Heinz StockingerContent integration by Grégoire Rossier and Vassilios Ioannidis Problem based learning, Programming, Unix Bench biologists Clinical Scientists Graduate Students beginner bioinformaticians biocurators 2014-01-13 2017-10-09
ChIP-seq analysis using R - Experimental design and peak calling.

This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling.

Keywords: ChIP-Seq, Experimental-design, Peak-calling, Visualisation

ChIP-seq analysis using R - Experimental design and peak calling. https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-experimental-design-and-peak-calling-cfd4c18f-6c86-45ae-ab0b-630422c76af6 This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling. ChIP-Seq, Experimental-design, Peak-calling, Visualisation
ChIP-seq analysis using R

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a...

Keywords: ChIP-Seq, Experimental-design, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming

ChIP-seq analysis using R https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-5049bc9c-9bbb-4a6b-9244-37ed3980da0e ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This course is an introduction to ChIP-seq data, and data analysis mainly using R, some command line based peak-callers and online software. It provides a theoretical background and the means to perform peak calling and differential binding analysis. ChIP-Seq, Experimental-design, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming
Introduction to Biopython

This is a module from the "Python for Biologists" course. The module presents an introduction to Biopython. It shows how to deal with sequences and sequence records, how to download records from NCBI databases, how to run Blast and how to parse XML Blast outputs.

Keywords: Bioinformatics, Biopython, Programming, Python, Python biologists

Introduction to Biopython https://tess.elixir-europe.org/materials/introduction-to-biopython This is a module from the "Python for Biologists" course. The module presents an introduction to Biopython. It shows how to deal with sequences and sequence records, how to download records from NCBI databases, how to run Blast and how to parse XML Blast outputs. Bioinformatics, Biopython, Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists bioinformaticians 2013-11-04 2017-10-09
ChIP-seq analysis using R - Experimental design and peak calling.

This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling.

Keywords: ChIP-Seq, Experimental-design, Peak-calling, Visualisation

ChIP-seq analysis using R - Experimental design and peak calling. https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-experimental-design-and-peak-calling This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling. ChIP-Seq, Experimental-design, Peak-calling, Visualisation
ChIP-seq analysis using R - Quality Control

This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts.

Scientific topics: RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

ChIP-seq analysis using R - Quality Control https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-quality-control This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design
ChIP-seq analysis using R - File formats and QC

This lecture introduces the file formats of sequencing data before alignment and covers the general quality control of sequencing data focussing on RNA-Seq and ChIP-Seq.

Scientific topics: RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

ChIP-seq analysis using R - File formats and QC https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-file-formats-and-qc This lecture introduces the file formats of sequencing data before alignment and covers the general quality control of sequencing data focussing on RNA-Seq and ChIP-Seq. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design
ChIP-seq analysis using R - Quality Control Walkthrough

This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts.

Scientific topics: RNA-Seq

Keywords: ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design

ChIP-seq analysis using R - Quality Control Walkthrough https://tess.elixir-europe.org/materials/chip-seq-analysis-using-r-quality-control-walkthrough This practical illustrates steps that can be undertaken to assess the quality of the sequencing data. We will start from the fastq files and assess their quality in respect to potential contamination and technical artifacts. RNA-Seq ChIP-Seq, RNA-Seq, QC, Data-format, Experimental-design
Perl 1 Training Course - For Programming Beginners

A set of slides from The Sainsbury Laboratory Perl course for absolute beginners

Keywords: Perl, Programming

Perl 1 Training Course - For Programming Beginners https://tess.elixir-europe.org/materials/perl-1-training-course-for-programming-beginners A set of slides from The Sainsbury Laboratory Perl course for absolute beginners Perl, Programming Beginners Bench biologists 2014-07-03 2017-10-09
Using R with Python

This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented...

Keywords: Programming, Python, Python biologists

Using R with Python https://tess.elixir-europe.org/materials/using-r-with-python This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented are also provided. Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians bioinformaticians 2013-11-04 2017-10-09
Searching data using Python

This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and...

Keywords: Programming, Python, Python biologists

Searching data using Python https://tess.elixir-europe.org/materials/searching-data-using-python This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and how to use sets to find unique records in two datasets and remove redundancy.  Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Pattern Matching

This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological...

Keywords: Pattern matching, Programming, Python, Python biologists

Pattern Matching https://tess.elixir-europe.org/materials/pattern-matching This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological sequences and in regular text, such as PubMed abstracts. Exercises and suggested solutions are presented in a separate file. Pattern matching, Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Writing functions in Python programming

This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file. 

Scientific topics: Bioinformatics

Keywords: Programming, Python, Python biologists

Writing functions in Python programming https://tess.elixir-europe.org/materials/writing-functions-in-python-programming This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file.  Bioinformatics Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Python Programs

This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions. 

Keywords: Programming, Python, Python biologists

Python Programs https://tess.elixir-europe.org/materials/python-programs This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions.  Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Parsing data records using Python programming

This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list  data structure. The...

Keywords: Bioinformatics, Programming, Python, Python biologists, Record parsing

Parsing data records using Python programming https://tess.elixir-europe.org/materials/parsing-data-records-using-python-programming This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list  data structure. The text of exercises is provided in a separate file.  Bioinformatics, Programming, Python, Python biologists, Record parsing Biologists beginner bioinformaticians bioinformaticians programmers 2013-07-05 2017-10-09
Introduction to Unix

Introductory lecture to the Unix/Linux command-line Description of the computer shell and the command-line interface Differences between graphical and command-line interfaces The most commond Unix/Linux commands are provided    

Keywords: Bioinformatics, Programming, Unixlinux

Introduction to Unix https://tess.elixir-europe.org/materials/introduction-to-unix Introductory lecture to the Unix/Linux command-line Description of the computer shell and the command-line interface Differences between graphical and command-line interfaces The most commond Unix/Linux commands are provided     Bioinformatics, Programming, Unixlinux Anyone wants to start using the Unix/Linux OS 2013-07-04 2017-10-09