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21 materials found

Authors: allegra.via Via  or nekrut 


Data Manipulation - Collections: Multisample Analysis

A collection of microtutorials explaining data manipulation within Galaxy

Resource type: Tutorial

Data Manipulation - Collections: Multisample Analysis http://tess.elixir-uk.org/materials/data-manipulation-collections-multisample-analysis A collection of microtutorials explaining data manipulation within Galaxy
Data Manipulation - Collections: Using dataset collection

A collection of microtutorials explaining data manipulation within Galaxy Questions of the tutorial: - How to manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections

Resource type: Tutorial

Data Manipulation - Collections: Using dataset collection http://tess.elixir-uk.org/materials/data-manipulation-collections-using-dataset-collection A collection of microtutorials explaining data manipulation within Galaxy Questions of the tutorial: - How to manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections
User Interface and Features - Histories: Understanding Galaxy history system

A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - How do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories

Resource type: Tutorial

User Interface and Features - Histories: Understanding Galaxy history system http://tess.elixir-uk.org/materials/user-interface-and-features-histories-understanding-galaxy-history-system A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - How do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories
Assembly - Making sense of a newly assembled genome

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Making sense of a newly assembled genome http://tess.elixir-uk.org/materials/assembly-making-sense-of-a-newly-assembled-genome DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - I just assembled a genome. How does it compare with already sequenced genomes? - How do I find rearranged, inserted, or deleted regions? Objectives of the tutorial: - Identification of the most closely related genome to my new assembly - Perform sequence comparison to locate rearrangements - Identify genes located in deletions
Variant Analysis - Calling very rare variants

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - What frequency of variants is so low that it is obscured by sequencing error rate? - What are the different types of consensus sequences produced from duplex sequencing? Objectives of...

Resource type: Tutorial

Variant Analysis - Calling very rare variants http://tess.elixir-uk.org/materials/variant-analysis-calling-very-rare-variants Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - What frequency of variants is so low that it is obscured by sequencing error rate? - What are the different types of consensus sequences produced from duplex sequencing? Objectives of the tutorial: - Processing raw duplex sequencing data into consensus sequences - Find rare variants without relying on diploid assumptions
Variant Analysis - Calling variants in diploid systems

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to find variable sites in diploid genomes? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in human genome.

Resource type: Tutorial

Variant Analysis - Calling variants in diploid systems http://tess.elixir-uk.org/materials/variant-analysis-calling-variants-in-diploid-systems Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to find variable sites in diploid genomes? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in human genome.
Variant Analysis - Calling variants in non-diploid systems

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How does frequency of mitochondrial polymorphisms change from mother to child? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in bacteria,...

Resource type: Tutorial

Variant Analysis - Calling variants in non-diploid systems http://tess.elixir-uk.org/materials/variant-analysis-calling-variants-in-non-diploid-systems Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How does frequency of mitochondrial polymorphisms change from mother to child? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.
Introduction to Galaxy Analyses - NGS data logistics

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to manipulate and process...

Resource type: Tutorial

Introduction to Galaxy Analyses - NGS data logistics http://tess.elixir-uk.org/materials/introduction-to-galaxy-ngs-data-logistics Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to manipulate and process NGS data Objectives of the tutorial: - Learn about Fastq, SAM, and BAM.
Transcriptomics - Reference-based RNAseq data analysis (long)

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How to perform analysis of RNAseq data when reference genome is available? Objectives of the tutorial: - Learns basic concepts of RNAseq analysis

Resource type: Tutorial

Transcriptomics - Reference-based RNAseq data analysis (long) http://tess.elixir-uk.org/materials/transcriptomics-reference-based-rnaseq-data-analysis-long Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How to perform analysis of RNAseq data when reference genome is available? Objectives of the tutorial: - Learns basic concepts of RNAseq analysis
Assembly - Unicycler Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Unicycler Assembly http://tess.elixir-uk.org/materials/assembly-unicycler-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - I have short reads and long reads. How do I assemble a genome? Objectives of the tutorial: - Perform Quality Control on your reads - Perform a Small genome Assembly with Unicycler - Evaluate the Quality of the Assembly with Quast - Annotate the assembly with Prokka
Introduction to Galaxy Analyses - IGV Introduction

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Resource type: Tutorial

Introduction to Galaxy Analyses - IGV Introduction http://tess.elixir-uk.org/materials/galaxy-introduction-igv-introduction Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Introduction to Galaxy Analyses - Galaxy 101

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which coding exon has the...

Resource type: Tutorial

Introduction to Galaxy Analyses - Galaxy 101 http://tess.elixir-uk.org/materials/galaxy-introduction-galaxy-101 Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work
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 http://tess.elixir-uk.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
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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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
Linear Motifs and Phosphorylation Sites

This is a lecture on linear motifs and phophorylation sites (P-sites). Some materials from other lectures are reused. The lecture is basically about computational approaches to encode, predict, analyse, and use functional motifs and P-sites. Here you can find: A definition of linear motifs and...

Keywords: Bioinformatics

Linear Motifs and Phosphorylation Sites http://tess.elixir-uk.org/materials/linear-motifs-and-phosphorylation-sites This is a lecture on linear motifs and phophorylation sites (P-sites). Some materials from other lectures are reused. The lecture is basically about computational approaches to encode, predict, analyse, and use functional motifs and P-sites. Here you can find: A definition of linear motifs and P-sites Computational methods to identify them How you can represent and use them Resources and tools to deal with them Bioinformatics Biologists biocurators bioinformaticians 2013-07-16 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 http://tess.elixir-uk.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 http://tess.elixir-uk.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