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  • NGS Registry

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

    62 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
    7 upcoming events (405 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
    0 upcoming events (3 past events)
    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 (10 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

  • Birmingham Metabolomics Training Centre

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

    4 upcoming events (21 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

  • 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

  • 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.

  • 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
    0 upcoming events (1 past event)
    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

  • How to install or re-install McAfee Livesafe on your PC or Mac.

    Just because when you are attempting to introduce Mcafee Livesafe on your gadget, you need to...

    How to install or re-install McAfee Livesafe on your PC or Mac. https://tess.elixir-europe.org/content_providers/how-to-install-or-re-install-mcafee-livesafe-on-your-pc-or-mac Just because when you are attempting to introduce Mcafee Livesafe on your gadget, you need to enroll for McAfee Account. While Registering for the McAfee Account on the register window you will be approached to impart your some close to home data to Mcafee Community. On the off chance that you pick this default alternative, the Life safe item will get naturally set-up on your gadget with the typical procedure. In the event that you didn't pick that alternative you can actuate the Mcafee activate Livesafe later by picking the McAfee board and create or by signing in to your McAfee account On the off chance that you are a Mac User, Before Starting just opens the Download box, and affirm that the envelope doesn't have the past adaptation .dmg document of McAfee. In the event that you see any record there, simply rename that document. In the event that any past form of McAfee arrangement document is available in the downloads envelope it can make the Mac mount the wrong Setup record of McAfee and that will stop the item to Activate effectively. See the More Information area of this page for more data. Open the program and in the location bar simply type in their home.mcafee.com/activate, from the additional PC or macintosh you are attempting to introduce. 1. On the upper right corner, click on my record at that point sign in. 2. Type your McAfee login qualification i.e Your McAfee email and secret word. 3. On the off chance that you don't have the McAfee Account, click on would you say you are another client? After that click on Register 4. Now, and follow the on-screen prompts come to follow to make another record, and afterward sign in to your record. 5. On the off chance that you need the site treats to keep in the framework information of your client name later on, Select Remember me. Snap on My Account. 6. Pick the privilege Livesafe item membership, and afterward click on download. 7. Peruse the Complete End User License Agreement (EULA) and Select I Agree to acknowledge the terms and standards and proceed the download and establishment process. 8. Adhere to the On-Screen Instruction to introduce and arrange your Mcafee Antivirus /system/content_providers/images/000/000/134/original/mcafee_activate.jpg?1584882312

  • How to Fix 5 Most Common Network McAfee Security Threats

    The dangers of your own data getting ruptured have developed enormously as of late as even a few...

    How to Fix 5 Most Common Network McAfee Security Threats https://tess.elixir-europe.org/content_providers/how-to-fix-5-most-common-network-mcafee-security-threats The dangers of your own data getting ruptured have developed enormously as of late as even a few MNCs got ransomware introduced on their frameworks. A few associations face organize security-related issues without their own acknowledgment. At the point when these issues stayed uncertain, they make openings and vulnerabilities for breachers to assault an association's mcafee.com/activate security. This can bring about touchy data getting taken. The issues are very much an excessive amount to be shrouded in a solitary post, so here we will cover 5 of the most generally confronted organize security issues anybody can confront. 1: Unidentified Property on the Network Larger part of the organizations don't keep a total record of their IT resources that are bound with their system. This is an immense issue. On the off chance that the business doesn't have the foggiest idea what resources are on their system, at that point how might they be certain that their system security is sheltered? 2: User Account Benefits Abused It could be an innocent mix-up, as to send data on an inappropriate email address or to lose a gadget utilized grinding away. It could be a deliberate break or maltreatment of a client account. The issues that emerge from such dealings bargain your system's security the most. Since these issues emerge from inside the association, they are the hardest to catch and stop yet here are ways for you to limit the risk. Your organization can embrace the least benefit approach that keeps the representatives get to benefits to the base. The clients might have the option to get to the regions and areas which are required for the employments and that's it. 3: Unsecured Security Weaknesses The organizations typically get worried about endeavors known as Zero Day. These are the adventures which are as yet obscure to the clients; notwithstanding, zero-days are not the genuine issue. The genuine issue is known uncertain vulnerabilities. The most ideal way out of it is to deal with an exacting timetable for security fixes. Additionally, the endeavor should fix the issue when it is recognized. 4: Inadequate Management in IT Security It is another regular issue among undertakings. They don't get a well-suited measure of individuals in IT security the board. So regardless of whether the issues are getting distinguishes, they despite everything would not have the option to fix them so as to stop a rupture. The main answer for the issue is to keep up a certified security supervisory group, with sufficient individuals to satisfy the activity. 5: Low Depth in Defenses There will be days when regardless of your endeavors the assailant will rupture in. Be that as it may, how much harm they can do is up to you. The business should attempt to keep a www.mcafee.com/activate secure division to keep the parts separate carefully. So regardless of whether the assailant traverses one security, they would not have the option to get a significant part of the fundamental data. Keep the patches fixed, and the framework composed so your delicate data remains safe and inside your insight.

  • Digital Marketing Agency & Online Branding Company!

    Dakshraj Enterprise is a digital marketing agency & online branding company in Kolkata, India....

    0 upcoming events (1 past event)
    Digital Marketing Agency & Online Branding Company! https://tess.elixir-europe.org/content_providers/digital-marketing-agency-online-branding-company Dakshraj Enterprise is a digital marketing agency & online branding company in Kolkata, India. And we have been providing professional digital marketing and web designing services for over 10 years. We deliver unmatched quality services like search engine optimization (SEO), social media optimization (SMO), PPC management (Google Ads & Bing Ads), content marketing strategy & many more. Combining our solid business domain experience, technical expertise along with profound knowledge of the latest tech industry trends and quality-driven delivery model we offer progressive end-to-end web & marketing solutions. /system/content_providers/images/000/000/137/original/digital-marketing-search-engine-optimization-marketing-content-royalty-free-thumbnail.jpg?1587530738

  • Survey To Earn

    Do you really want to make money online easily or how about making additional money without...

    Survey To Earn https://tess.elixir-europe.org/content_providers/survey-to-earn Do you really want to make money online easily or how about making additional money without getting into any kind of hassle? If this is the case then you’re certainly at the right platform. Survey to earn is one of the most user-friendly websites that allows you to make money online by simply answering a few questions in paid surveys. Now this is easy, so it’s best to give it a go. Try your luck and you won’t regret your decision. <a href="https://www.surveytoearn.com/">hgddsgjf</a> /system/content_providers/images/000/000/143/original/265b1184cdfc341d454d2e9d1e94795f.jpg?1590986339

  • Survey To Earn

    Do you really want to make money online easily or Want to earn Additional Money without getting...

    Survey To Earn https://tess.elixir-europe.org/content_providers/survey-to-earn-edcbaea7-9c73-4530-9433-bca38b37c33a Do you really want to make money online easily or Want to earn Additional Money without getting into any kind of hassle? If this is the case then you’re certainly on the right platform. Survey to earn is one of the most user-friendly & Worlds <a href="http://blog.surveytoearn.com/make-money/top-paid-surveys-websites/">Top Paid survey website</a> that allows you to make money online by simply answering a few questions in paid surveys. Now, this is easy, so it’s best to give it a go. Try your luck and you won’t regret your decision. /system/content_providers/images/000/000/144/original/265b1184cdfc341d454d2e9d1e94795f.jpg?1590986595
    • Showing 30 materials out of 137. 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 11 upcoming events. Found 444 past events. View all results.

    • Data Science School: Machine learning applications for life sciences

      21 - 24 September 2020

      Cambridge, United Kingdom

      Elixir node event
      Data Science School: Machine learning applications for life sciences https://tess.elixir-europe.org/events/data-science-school-machine-learning-applications-for-life-sciences This School aims to familiarise biomedical students and researchers with principles of Data Science. Focusing on utilising machine learning algorithms to handle biomedical data, it will cover: effects of experimental design, data readiness, pipeline implementations, machine learning in Python, and related statistics, as well as Gaussian Process models. Providing practical experience in the implementation of machine learning methods relevant to biomedical applications, including Gaussian processes, we will illustrate best practices that should be adopted in order to enable reproducibility in any data science application. This event is sponsored by [Cambridge Centre for Data-Driven Discovery (C2D3)](https://www.bigdata.cam.ac.uk/). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3357195&amp;course-title=Data%20Science%20School).'' 2020-09-21 09:00:00 UTC 2020-09-24 14:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Machine learning Bioinformatics University of Cambridge Bioinformatics Training [] Students and researchers from life-sciences or biomedical backgroundswho haveor will shortly havethe need to apply the techniques presented during the course to biomedical data.The course is open to Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals<span style="color:#FF0000">Please note that all participants attending this course will be charged a registration fee. <span style="color:#0000FF"> Non-members of the University of Cambridge to pay £400. </span style> <span style="color:#0000FF">All Members of the University of Cambridge to pay £200. </span style> <span style="color:#FF0000">A booking will only be approved and confirmed once the fee has been paid in full.</span style> workshops_and_courses [] HDRUK

    • Introduction to Metabolomics for the Microbiologist

      7 - 9 October 2020

      Birmingham, United Kingdom

      Elixir node event
      Introduction to Metabolomics for the Microbiologist https://tess.elixir-europe.org/events/introduction-to-metabolomics-for-the-microbiologist-5b05fb3a-a745-44e2-80ec-b515cec15eee This three-day course introduces how untargeted metabolomics can be applied to study microbial systems in academic and industrial research. The course provides an overview of the metabolomics pipeline, experimental... 2020-10-07 09:15:00 UTC 2020-10-09 16:00:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []

    • Metabolomics with the Q Exactive

      2 - 4 November 2020

      Birmingham, United Kingdom

      Elixir node event
      Metabolomics with the Q Exactive https://tess.elixir-europe.org/events/metabolomics-with-the-q-exactive-920cedd9-d06b-4970-9619-562b1e06ae2f This 3-day course introduces you to using the Q Exactive mass spectrometer in your metabolomics investigations. The course is led by experts in the field of metabolomics and includes lectures, laboratory sessions... 2020-11-02 09:00:00 UTC 2020-11-04 15:45:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []

    • Metabolite Identification with the Q Exactive and LTQ Orbitrap Elite

      5 - 6 November 2020

      Birmingham, United Kingdom

      Elixir node event
      Metabolite Identification with the Q Exactive and LTQ Orbitrap Elite https://tess.elixir-europe.org/events/metabolite-identification-with-the-q-exactive-and-ltq-orbitrap-elite-46935e8e-1043-4de4-8494-74207989c510 This 2-day course provides a hands-on approach to teach attendees about the latest techniques and tools available to perform metabolite identification in non-targeted metabolomics studies. The course is led by experts... 2020-11-05 09:00:00 UTC 2020-11-06 17:30:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []

    • Multiple Biofluid and Tissue Types, From Sample Preparation to Analysis Strategies for Metabolomics

      23 - 25 September 2020

      Birmingham, United Kingdom

      Elixir node event
      Multiple Biofluid and Tissue Types, From Sample Preparation to Analysis Strategies for Metabolomics https://tess.elixir-europe.org/events/multiple-biofluid-and-tissue-types-from-sample-preparation-to-analysis-strategies-for-metabolomics-7d1a21e4-32f0-4e9a-a67c-32d2932fa6f5 This 3-day course provides a theoretical overview and hands-on training to apply multiple sample preparation and UPLC-MS methods to characterise the metabolomes of complex biological samples using the mass spec... 2020-09-23 09:00:00 UTC 2020-09-25 15:30:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []

    • Ensembl REST API workshop

      2 September 2020

      Cambridge, United Kingdom

      Elixir node event
      Ensembl REST API workshop https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-c3f269e2-c30f-4a2d-b719-a822af0359c5 The [Ensembl project](http://www.ensembl.org/) provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl [REST APIs](http://rest.ensembl.org/), including understanding the major endpoints and how to write scripts to call them. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3351102&amp;course-title=Ensembl%20REST%20API%20Workshop).'' 2020-09-02 08:30:00 UTC 2020-09-02 14:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Bioinformaticians and wet-lab biologists who can programGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK

    • An Introduction to MATLAB for biologists (ONLINE LIVE TRAINING)

      29 - 30 June 2020

      Cambridge, United Kingdom

      Elixir node event
      An Introduction to MATLAB for biologists (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/an-introduction-to-matlab-for-biologists-56fe486a-5d6b-46d2-ab62-33a6bf501fb4 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 aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts. 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 Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3398010&amp;course-title=An%20Introduction%20to%20MATLAB).'' 2020-06-29 08:30:00 UTC 2020-06-30 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics 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

    • Introduction to R for Biologists (ONLINE LIVE TRAINING)

      22 - 23 June 2020

      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-494464b5-8cde-48c4-b1b0-5b91df43e569 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=3338957&amp;course-title=Introduction%20to%20R%20for%20Biologists).'' 2020-06-22 08:30:00 UTC 2020-06-23 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)

      24 - 26 June 2020

      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-18be52a3-28d7-4f66-a339-edd4cc7f6dcb 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 be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes. 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=3401732&amp;course-title=An%20Introduction%20to%20Machine%20Learning).'' 2020-06-24 08:30:00 UTC 2020-06-26 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 Bioinformatics 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

    • Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING)

      1 - 3 July 2020

      Cambridge, United Kingdom

      Elixir node event
      Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/analysis-of-bulk-rna-seq-data-online-live-training 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. The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data. This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq. 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=3392203&amp;course-title=Analysis%20of%20bulk%20RNA-seq%20data).'' 2020-07-01 08:30:00 UTC 2020-07-03 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR RNA-Seq Data mining Transcriptomics Data visualisation Functional genomics Bioinformatics 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

    • Using the Ensembl Genome Browser

      1 September 2020

      Cambridge, United Kingdom

      Elixir node event
      Using the Ensembl Genome Browser https://tess.elixir-europe.org/events/using-the-ensembl-genome-browser-467135ab-7028-4d4f-8a24-bbffa5548b3b The [Ensembl Project](http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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=3351117&amp;course-title=Using%20the%20Ensembl%20Genome%20Browser).'' 2020-09-01 08:30:00 UTC 2020-09-01 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Gene transcripts Gene structure Bioinformatics 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