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  • NGS Registry

    GitLab repository and its Wiki companion containing a collection of training materials for...

    60 training materials
    NGS Registry https://tess.elixir-europe.org/content_providers/ngs-registry GitLab repository and its Wiki companion containing a collection of training materials for teaching next generation sequencing data analysis.

  • University of Cambridge Bioinformatics Training

    We offer a broad range of undergraduate and postgraduate hands-on training courses focused on...

    4 training materials
    6 upcoming events (466 past events)
    University of Cambridge Bioinformatics Training https://tess.elixir-europe.org/content_providers/university-of-cambridge-bioinformatics-training We offer a broad range of undergraduate and postgraduate hands-on training courses focused on bioinformatics and computational biology. These training activities aim at enabling life scientists to effectively handle and interpret biological data. /system/content_providers/images/000/000/057/original/logo.png?1477998653

  • Bioinformatics and Biomathematics Training Hub

    The Bioinformatics and Biomathematics Training Hub (BBTH) is a BBSRC-funded collaborative project...

    62 training materials
    Bioinformatics and Biomathematics Training Hub https://tess.elixir-europe.org/content_providers/bioinformatics-and-biomathematics-training-hub The Bioinformatics and Biomathematics Training Hub (BBTH) is a BBSRC-funded collaborative project to coordinate the development and sharing of training materials and expertise across the UK’s National Institutes of Bioscience (NIB — http://www.nib.ac.uk/) for the increasingly important areas of bioinformatics and biomathematics. Guided by our NIB partners, researcher surveys, and interactions with interested bodies such as Elixir-UK, we will work to ensure that best use is made of existing assets and capabilities, that best practice is shared across the NIB, and that redundant effort is minimised going forwards. /system/content_providers/images/000/000/061/original/BBTH_logo.png?1480508618

  • Edinburgh Genomics

    The explosion in new sequencing technologies has changed genomics from being the province of a...

    0 upcoming events (12 past events)
    Edinburgh Genomics https://tess.elixir-europe.org/content_providers/edinburgh-genomics The explosion in new sequencing technologies has changed genomics from being the province of a few to being a key part in many research programmes. To enable researchers to analyse their next generation sequencing data themselves, Edinburgh Genomics offers a range of hands-on bioinformatics workshops. /system/content_providers/images/000/000/076/original/unnamed.png?1494410486

  • University of Leicester Bioinformatics and Biostatistics Analysis Support Hub (BBASH)

    The ongoing development of next generation sequencing (NGS) technologies has meant that vast...

    0 upcoming events (2 past events)
    University of Leicester Bioinformatics and Biostatistics Analysis Support Hub (BBASH) https://tess.elixir-europe.org/content_providers/university-of-leicester-bioinformatics-and-biostatistics-analysis-support-hub-bbash The ongoing development of next generation sequencing (NGS) technologies has meant that vast amounts of sequencing data is being produced, with researchers increasingly wanting the capability and knowledge to analyse their own data. Over the past 3 years BBASH has developed a number of 1, 2 and 3 day hands-on, NGS analysis workshops designed specificially to meet the needs of laboratory based researchers with little or no experience of NGS data analysis and command line tools. The workshops are held at the University of Leicester's state of the art College Court Conference Centre and consist of introductory presentations followed by practical sessions where delegates will gain hands-on experience of analysing and interpreting real data. The BBASH trainers are University of Leicester bioinformaticians or researchers with many years experience in bioinformatics and bioinformatics training, having delivered many workshops across the UK and Europe. /system/content_providers/images/000/000/086/original/BBASHlogo.png?1509536575

  • Birmingham Metabolomics Training Centre

    Providing training to empower the next generation of metabolomics researchers. The Birmingham...

    1 upcoming event (25 past events)
    Birmingham Metabolomics Training Centre https://tess.elixir-europe.org/content_providers/birmingham-metabolomics-training-centre Providing training to empower the next generation of metabolomics researchers. The Birmingham Metabolomics Training Centre provides training to the metabolomics community in both analytical and computational methods. The training centre partners with both the Phenome Centre Birmingham and the NERC Biomolecular Analysis Facility to provide vocational training courses in clinical and environmental metabolomics. We offer a combination of both face-to-face and online courses. The Birmingham Metabolomics Training Centre is directed by Dr Warwick Dunn, Professor Mark Viant, Dr Ralf Weber and Dr Catherine Winder. /system/content_providers/images/000/000/084/original/12106_BMTC_lock-up_AW-01.jpg?1508159124

  • Earlham Institute

    The Earlham Institute (EI) is a research institute focused on exploring living systems by...

    Earlham Institute https://tess.elixir-europe.org/content_providers/earlham-institute The Earlham Institute (EI) is a research institute focused on exploring living systems by applying computational science and biotechnology to answer ambitious biological questions and generate enabling resources. /system/content_providers/images/000/000/145/original/Earlham_Square.png?1612798057

  • Jalview

    Jalview (www.jalview.org) is free-to-use sequence alignment and analysis visualisation software...

    0 upcoming events (1 past event)
    Jalview https://tess.elixir-europe.org/content_providers/jalview Jalview (www.jalview.org) is free-to-use sequence alignment and analysis visualisation software that links genomic variants, protein alignments and 3D structure. Protein, RNA and DNA data can be directly accessed from public databases (e.g. Pfam, Rfam, PDB, UniProt and ENA etc.). Jalview has editing and annotation functionality within a fully integrated, multiple window interface. The sequence alignment programs Clustal Omega, Muscle, MAFFT, ProbCons, T-COFFEE, ClustalW, MSA Prob and GLProb can be run directly from within Jalview. Jalview integrates protein secondary structure prediction (JPred), generate trees, assesses consensus and conservation across sequence families. Journal quality figures can be generated from the results. The Jalview Desktop will run on Mac, MS Windows, Linux and any other platform that supports Java. It has been developed in Geoff Barton's group (www.compbio.dundee.ac.uk) in the School of Life Sciences (www.lifesci.dundee.ac.uk) at the University of Dundee with funding from the BBSRC and the Wellcome Trust. /system/content_providers/images/000/000/091/original/logo-boxg.png?1524735946

  • InterMine

    InterMine integrates biological data sources, making it easy to query and analyse data.

    8 training materials
    InterMine https://tess.elixir-europe.org/content_providers/intermine InterMine integrates biological data sources, making it easy to query and analyse data. /system/content_providers/images/000/000/095/original/intermine-300x37.png?1530283825

  • FAIRsharing

    FAIRsharing is a web-based, searchable portal of three interlinked registries, containing both...

    1 training material
    FAIRsharing https://tess.elixir-europe.org/content_providers/fairsharing FAIRsharing is a web-based, searchable portal of three interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards, databases and data policies, combined with an integrated view across all three types of resource. By registering your resource on FAIRsharing, you not only gain credit for your work, but you increase its visibility outside of your direct domain, so reducing the potential for unnecessary reinvention and proliferation of standards and databases. /system/content_providers/images/000/000/109/original/FAIRsharing_logo.png?1544089458
    • Showing 30 materials out of 135. View all results.
    NGS introduction to sequencing platforms

    This sub-module gives an overview of the most used sequencing platforms and their applications.

    Keywords: HTS-introduction

    NGS introduction to sequencing platforms https://tess.elixir-europe.org/materials/ngs-introduction-to-sequencing-platforms This sub-module gives an overview of the most used sequencing platforms and their applications. HTS-introduction
    Quality Control

    This is an introduction to the tools available for performing the technical QA of RNA-Seq data and to their results, singling out possible common caveats.

    Scientific topics: RNA-Seq

    Keywords: FASTQ, RNA-Seq, Pre-processing, QC

    Quality Control https://tess.elixir-europe.org/materials/quality-control This is an introduction to the tools available for performing the technical QA of RNA-Seq data and to their results, singling out possible common caveats. RNA-Seq FASTQ, RNA-Seq, Pre-processing, QC
    Exploratory analysis and downstream analysis

    This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods...

    Keywords: Statistical-model, Exploratory-analysis

    Exploratory analysis and downstream analysis https://tess.elixir-europe.org/materials/exploratory-analysis-and-downstream-analysis This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods developed (e.g.) for microarray data. Statistical-model, Exploratory-analysis
    NGS introduction to file formats

    This sub-module gives an overview of the most used file formats in Next Generation Sequencing analysis

    Keywords: HTS-introduction, FASTQ, BAM, VCF, WIG, CRAM, GFF3

    NGS introduction to file formats https://tess.elixir-europe.org/materials/ngs-introduction-to-file-formats This sub-module gives an overview of the most used file formats in Next Generation Sequencing analysis HTS-introduction, FASTQ, BAM, VCF, WIG, CRAM, GFF3
    EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014

    No description available

    Scientific topics: RNA-Seq

    Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

    EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014 https://tess.elixir-europe.org/materials/embo-high-throughput-sequencing-data-analysis-cambridge-uk-2014 No description available RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
    Introduction to HTS

    No description available

    Keywords: HTS-introduction

    Introduction to HTS https://tess.elixir-europe.org/materials/introduction-to-ngs No description available HTS-introduction
    Lecture slides for the course RNA-seq data analysis with Chipster

    This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015.

    Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

    Lecture slides for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/lecture-slides-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
    Annotation

    This introduces to the different sources of genomic and genic annotation and to their most commonly used format. It also introduces how to ensure that the used annotation are not a source of bias in downstream analyses.

    Scientific topics: RNA-Seq

    Keywords: GFF3, Populus-tremula, RNA-Seq, Annotation

    Annotation https://tess.elixir-europe.org/materials/annotation This introduces to the different sources of genomic and genic annotation and to their most commonly used format. It also introduces how to ensure that the used annotation are not a source of bias in downstream analyses. RNA-Seq GFF3, Populus-tremula, RNA-Seq, Annotation
    Alignment

    Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales.

    Scientific topics: RNA-Seq

    Keywords: BAM, Populus-tremula, RNA-Seq, QC, Alignment

    Alignment https://tess.elixir-europe.org/materials/alignment Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales. RNA-Seq BAM, Populus-tremula, RNA-Seq, QC, Alignment
    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, QC, Data-format, Alignment, Peak-calling, Differential-binding, Visualisation, Annotation

    ChIP-seq analysis using R https://tess.elixir-europe.org/materials/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 theoretical background and the means to perform peak calling and differential binding analysis. ChIP-Seq, Experimental-design, QC, Data-format, Alignment, Peak-calling, Differential-binding, Visualisation, Annotation
    Day 2 - RNA-Seq Analysis

    Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser.

    Keywords: Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing

    Day 2 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-2-rna-seq-analysis Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser. Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing
    RNA-seq module Frederik Coppens

    All material concerning RNA-seq analysis

    Scientific topics: RNA-Seq

    Keywords: RNA-Seq, Alignment, BAM, FASTQ, Feature-summarisation, Pre-processing, QC

    RNA-seq module Frederik Coppens https://tess.elixir-europe.org/materials/rna-seq-module-frederik-coppens All material concerning RNA-seq analysis RNA-Seq RNA-Seq, Alignment, BAM, FASTQ, Feature-summarisation, Pre-processing, QC
    Introduction to NGS and RNA-seq

    No description available

    Keywords: HTS-introduction, Data-format, Alignment, Differential-expression, Feature-summarisation, QC

    Introduction to NGS and RNA-seq https://tess.elixir-europe.org/materials/introduction-to-ngs-and-rna-seq No description available HTS-introduction, Data-format, Alignment, Differential-expression, Feature-summarisation, QC
    Data objects for R practice codes

    This RData file contains small R objects to use in the [introR.R practice questions](introR.R)

    Keywords: R-programming

    Data objects for R practice codes https://tess.elixir-europe.org/materials/data-objects-for-r-practice-codes This RData file contains small R objects to use in the [introR.R practice questions](introR.R) R-programming
    Day 1 - RNA-Seq Analysis

    Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer.

    Keywords: Alignment, BAM, FASTA, FASTQ, QC

    Day 1 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-1-rna-seq-analysis Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer. Alignment, BAM, FASTA, FASTQ, QC
    Exercises for the course RNA-seq data analysis with Chipster

    This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015.

    Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

    Exercises for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/exercises-for-the-course-rna-seq-data-analysis-with-chipster This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
    Guidelines for this folder

    No description available

    Guidelines for this folder https://tess.elixir-europe.org/materials/guidelines-for-this-folder No description available
    Differential expression analysis on the Robinson, Delhomme et al. dataset.

    A differential expression analysis conducted on the **[Robinson, Delhomme et al., dataset](https://microasp.upsc.se/ngs_trainers/Materials/blob/master/Datasets/Robinson-Delhomme-Populus-tremula-shows-no-evidence-of-sexual-dimorphism.md)**. The dataset has 17 samples and 2 important meta-data: the...

    Scientific topics: RNA-Seq

    Keywords: RNA-Seq, Differential-expression, R-programming, Statistical-model

    Differential expression analysis on the Robinson, Delhomme et al. dataset. https://tess.elixir-europe.org/materials/differential-expression-analysis-on-the-robinson-delhomme-et-al-dataset A differential expression analysis conducted on the **[Robinson, Delhomme et al., dataset](https://microasp.upsc.se/ngs_trainers/Materials/blob/master/Datasets/Robinson-Delhomme-Populus-tremula-shows-no-evidence-of-sexual-dimorphism.md)**. The dataset has 17 samples and 2 important meta-data: the sample sex and year of collection. The goal is to test whether genes are involved in different processes based on the sex of the tree; _i.e._ is there a sexual dimorphism in _Populus tremula_ trees. It has indeed been hypothesized that male tree should be taller so as to spread their pollen further, whereas female would be more resistant to pests and diseases. The existing literature is contradictory, however it resulted from studies where plants were grown in controlled environment. In the present dataset, plant samples were collected in the wild, at a 2 years interval. The latter is a very important factor in the analysis as the 'year effect' is a strong confounding factor that hides the 'sex effect'. The present tutorial, hence, introduces a differential-expression analysis, but goes further by adressing confounding factors and how to _block_ them in an analysis. It is a good dataset to remind trainees that they should always be critical towards the conclusion they draw from their data. RNA-Seq RNA-Seq, Differential-expression, R-programming, Statistical-model
    Edinburgh genomics introduction to RNA-seq data analysis

    No description available

    Edinburgh genomics introduction to RNA-seq data analysis https://tess.elixir-europe.org/materials/edinburgh-genomics-introduction-to-rna-seq-data-analysis No description available
    Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material

    Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and...

    Scientific topics: RNA-Seq

    Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

    Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material https://tess.elixir-europe.org/materials/nicolas-delhomme-bastian-schiffthaler-october-2014-embo-course-material Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and reproduces the Differential Expression analysis conducted in Robinson, Delhomme et al., 2014. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
    Introduction to R and Bioconductor lecture

    This lecture gives an overview of the R and Bioconductor projects, plus the basics of R object types and programming language structure.

    Keywords: R-programming

    Introduction to R and Bioconductor lecture https://tess.elixir-europe.org/materials/introduction-to-r-and-bioconductor-lecture This lecture gives an overview of the R and Bioconductor projects, plus the basics of R object types and programming language structure. R-programming
    Populus tremula shows no evidence of sexual dimorphism

    **Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and...

    Scientific topics: RNA-Seq

    Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression

    Populus tremula shows no evidence of sexual dimorphism https://tess.elixir-europe.org/materials/populus-tremula-shows-no-evidence-of-sexual-dimorphism **Background:** Although the majority of plant species are co-sexual, being either monoecious or hermaphroditic, a significant number are dioecious, having separate male and female individuals. Evolutionary theory suggests that males and females may develop sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximise reproductive success and fitness. The establishment of such sexual dimorphism would result in changes in gene expression patterns in non-floral organs. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression
    RNA-seq module Eija Korpelainen

    All material concerning RNA-seq data analysis with Chipster

    Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

    RNA-seq module Eija Korpelainen https://tess.elixir-europe.org/materials/rna-seq-module-eija-korpelainen All material concerning RNA-seq data analysis with Chipster FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
    Differential expression analysis

    This lecture covers the process from count matrix to statistical analysis results (differential expression). More specifically, it covers experimental design, normalization, statistical modeling and parameter estimation, multiple hypothesis testing and a more detailed look at some of the most...

    Keywords: Differential-expression, Statistical-model

    Differential expression analysis https://tess.elixir-europe.org/materials/differential-expression-analysis This lecture covers the process from count matrix to statistical analysis results (differential expression). More specifically, it covers experimental design, normalization, statistical modeling and parameter estimation, multiple hypothesis testing and a more detailed look at some of the most common differential expression methods as well as a comparison between them. Differential-expression, Statistical-model
    Material provided by Charlotte Soneson

    This folder contains material provided by Charlotte Soneson. The following material is included:

    Scientific topics: RNA-Seq

    Keywords: RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis

    Material provided by Charlotte Soneson https://tess.elixir-europe.org/materials/material-provided-by-charlotte-soneson This folder contains material provided by Charlotte Soneson. The following material is included: RNA-Seq RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis
    RNA-Seq Analysis with Biocluster and R

    Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it

    Scientific topics: RNA-Seq

    Keywords: RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model

    RNA-Seq Analysis with Biocluster and R https://tess.elixir-europe.org/materials/rna-seq-analysis-with-biocluster-and-r Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it RNA-Seq RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model
    Preprocessing RNA-Seq data

    Quality assessment and preprocessing of RNA-seq data. Description of FastQ format

    Keywords: Pre-processing

    Preprocessing RNA-Seq data https://tess.elixir-europe.org/materials/preprocessing Quality assessment and preprocessing of RNA-seq data. Description of FastQ format Pre-processing
    Intro to R and Bioconductor

    R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the...

    Keywords: Prerequisite, R-programming

    Intro to R and Bioconductor https://tess.elixir-europe.org/materials/intro-to-r-and-bioconductor R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the basic skills that will be needed before using R to analyze NGS data. Prerequisite, R-programming
    Prerequisite

    No description available

    Scientific topics: Statistics and probability

    Keywords: Unix, Linux, R-programming, Statistics

    Prerequisite https://tess.elixir-europe.org/materials/prerequisite No description available Statistics and probability Unix, Linux, R-programming, Statistics
    Tutorial

    This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided.

    Scientific topics: RNA-Seq

    Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming

    Tutorial https://tess.elixir-europe.org/materials/tutorial This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming
    Showing 6 upcoming events. Found 506 past events. View all results.

    • Introduction to R for Biologists (ONLINE LIVE TRAINING)

      1 - 2 June 2021

      Cambridge, United Kingdom

      Elixir node event
      Introduction to R for Biologists (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/introduction-to-r-for-biologists-online-live-training-d32d6180-5248-473e-afe6-6a3f150f8c14 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3894005&course-title=Introduction%20to%20R%20for%20Biologists).'' 2021-06-01 08:30:00 UTC 2021-06-02 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK

    • Metabolomics Data Processing and Data Analysis

      7 June - 2 July 2021

      Elixir node event
      Metabolomics Data Processing and Data Analysis https://tess.elixir-europe.org/events/metabolomics-data-processing-and-data-analysis-600f05c6-102c-4a4d-bece-76bea2435d8d #Content Overview This online course explores the tools and approaches that are used to process and analyse metabolomics data. You will investigate the challenges that are typically encountered in the analysis of metabolomics data, and provide solutions to overcome these problems. #Topics Covered * An introduction to metabolomics * An overview of the untargeted metabolomics workflow * The influence of experimental design and data acquisition on data analysis and data quality * An overview of processing NMR data * Processing direct infusion mass spectrometry data with a hands-on exercise * Processing liquid chromatography-mass spectrometry data with hands-on exercises * Reporting standards and data repositories * Data analysis, detecting outliers and drift, and pre-treatment methods * Univariate data analysis with a hands-on exercise * Multivariate data analysis (including unsupervised and supervised approaches) with hands-on exercises * The importance of statistical validation of results * Computational approaches for metabolite identification and translation of results into biological knowledge with hands-on exercises * What are the future challenges for data processing and analysis in metabolomics #Software used during the course * Galaxy to process direct infusion mass spectrometry data * XCMS online to process liquid chromatography – mass spectrometry data * MetaboAnalyst in the univariate and multivariate data analysis exercises * Metabolite annotation using PUTMEDID_ID operating in the Taverna workflow environment #Level The course would be ideally suited to MSc / PhD students or scientists who are in the early stages of analysing metabolomics data. No previous knowledge of the data processing and statistical analysis approaches is assumed, but a basic understanding of the metabolome, and the analytical techniques applied in the metabolomics field would be beneficial. A pre-course recommended reading list will be provided. 2021-06-07 09:00:00 UTC 2021-07-02 23:59:00 UTC Metabolomics [] [] [] workshops_and_courses [] MetabolomicsData AnalysisData processing

    • Next Generation Sequencing Platforms and Bioinformatics Analysis (ONLINE LIVE TRAINING)

      8 - 9 June 2021

      Cambridge, United Kingdom

      Elixir node event
      Next Generation Sequencing Platforms and Bioinformatics Analysis (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/next-generation-sequencing-platforms-and-bioinformatics-analysis-online-live-training-77685f58-eb95-4e6a-bd29-f4a51511cba8 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. Day 1 will introduce you to next generation sequencing technologies (NGS) and how they work, providers, common bioinformatics workflows, standardised file types, quality control. This session will include an introduction to Galaxy. [Galaxy](https://galaxyproject.org/) is an open, web-based platform for data-intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses. Day 2 will be hands-on practicals on using Galaxy to explore sequencing quality control, before and after removal of low quality samples. This forms the core of all NGS analyses and this day will conclude with how this data pipes into gene expression studies, variant calling and genome assemblies. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3894975&course-title=NGS%20Platforms%20and%20Bioinformatics%20Analysis).'' 2021-06-08 08:00:00 UTC 2021-06-09 11:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Biologistswet-lab scientistsbioinformatics and other life scientists planning to work with next-generation sequencing data.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK

    • Complex Network Analysis for Biologists (ONLINE LIVE TRAINING)

      7 June 2021

      Cambridge, United Kingdom

      Elixir node event
      Complex Network Analysis for Biologists (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/complex-network-analysis-for-biologists-online-live-training PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. Complex natural systems permeate many aspects of everyday life—including human intelligence, social media, biomedicine, agriculture, economics, even our personal and professional relationships. The past decade has seen intensification of research into structural and dynamical properties of complex networks. This course will introduce the basic principles of network theory, and hands-on DIY Network analysis using Cytoscape, one of the most widely used global platforms for construction and analysis of biomolecular networks such as gene regulatory interactions, protein complexes, hydrogen-bonding meshwork in active sites and neuronal networks. The aim is to conceptualize your own textual, tabular or genomic datasets as networks, and to understand how simple topological features can help to decipher complex properties of systems and processes. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3879479&course-title=Complex%20Network%20Analysis%20for%20Biologists).'' 2021-06-07 08:30:00 UTC 2021-06-07 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] This tutorial is basic and requires no prior knowledge of any coding language or software.Cytoscape will have to be downloaded and installed on your device for the practical sessions.Suitable for students and early career researcherspostdocs.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK

    • An Introduction to Solving Biological Problems with Python (ONLINE LIVE TRAINING)

      10 - 11 June 2021

      Cambridge, United Kingdom

      Elixir node event
      An Introduction to Solving Biological Problems with Python (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-python-online-live-training-5aee2538-c5b5-42f7-9ea6-1ad0d1795852 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core concepts of Python including Python syntax, data structures and reading/writing files. These are illustrated by a series of example programs. Upon completion of the course, participants will be able to write simple Python programs. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3894072&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20Python).'' 2021-06-10 08:30:00 UTC 2021-06-11 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK

    • An Introduction to Machine Learning (ONLINE LIVE TRAINING)

      14 - 16 July 2021

      Cambridge, United Kingdom

      Elixir node event
      An Introduction to Machine Learning (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/an-introduction-to-machine-learning-online-live-training-23883bfb-5089-4a89-93be-a3d28db78354 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3916414&course-title=An%20Introduction%20to%20Machine%20Learning).'' 2021-07-14 08:30:00 UTC 2021-07-16 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Machine learning Data mining University of Cambridge Bioinformatics Training [] This is aimed at life scientists with little or no experience in machine learning and that are looking at implementing these approaches in their research.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK