Services - Informatics Analysis

Events‌ and Workshops

The Centre for Genomic Research frequently hosts informatics workshops as well as seminars about the latest technology available from the major companies in the NGS market.

R for beginners – An introduction course

11th to 13th of September 2019, University of Liverpool

  • Registration for the next R for beginners course! As in previous iterations in this 3 full day course we will cover an assortment of topics toDay 1: foundations of R: get familiar with R, R studio, operators, variables, functions, directories and the script editor
  • Day 2: visualisation in  basic R (boxplots, scatterplots, line graphs and  histograms) and ggplot2 (same types of plots and also manipulation of data for use within this package as well as simple linear regression)
  • Day 3: Introduction to statistical analyses in R: univariate statistics (choosing the right test, checking data assumptions, calculating and extracting the values to report in publications) and Principal Component Analysis (calculation and visualisation with ggplot2)
  • Extra materials: Introduction to the Tidyverse

The course has been designed to introduce R from the very basics. Therefore applicants do not need any prior experience to attend, just the desire to learn R. Real life examples with bioinformatic applications are included.

As always places are limited. Resgistration can be completed by filling this form.

 

 

Previous events

  • Python for Biologists 12th-15th August 2019, University of Liverpool

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    The workshop will take place over 5 days. Each day will consist of 2 half-day sessions, each consisting of a ~1 hour lecture followed by 2 hours of practical exercises. Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way.

    The instructor of the workshop is the Founder of Python for Biologists, Dr. Martin Jones. 

  • CGR Metagenomics 15th-17th May 2019

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    Centre for Genomic Research and Computational Biology Facility, University of Liverpool 

    This 3-day bioinformatics course is presented by the Centre for Genomic Research. It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

    16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 3-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

    Sequence data QC and preparation for downstream analyses
    Metagenomic shotgun sequence analysis.
    Taxonomic profiling (Kraken & Bracken)
    Metagenome assembly (MEGAHIT) and annotation (prodigal)
    Functional annotation (EggNOG)
    Data visualisation
    Analysis of 16S rRNA data with QIIME2
    Laboratory tour of sequencing laboratory
    Metagenome functional prediction using metagenetic data (PICRUSt)

     

    Feedbacks from partecipants:

    "Trainers were able to cater to the requirements of attendees irrespective of whether they had extensive knowledge of metagenomics or if they were new to the subject"

    "The handouts and working independently were great as it allowed me to work at my own pace and ask questions when needed"

  • CGR & NERC Metagenomics 11th-13th March 2019

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    Centre for Genomic Research and Computational Biology Facility, University of Liverpool 

    This 3-day bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

    16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 3-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

    Sequence data QC and preparation for downstream analyses
    Metagenomic shotgun sequence analysis.
    Taxonomic profiling (Kraken & Bracken)
    Metagenome assembly (MEGAHIT) and annotation (prodigal)
    Functional annotation (EggNOG)
    Data visualisation
    Analysis of 16S rRNA data with QIIME2
    Laboratory tour of sequencing laboratory
    Metagenome functional prediction using metagenetic data (PICRUSt)

     

    Feedbacks from partecipants:

    "It was obviously well thought out and taught by a lead instructor who has a flair for teaching as well as a deep understanding of the subject".

    "The workbooks are very detailed and should be a useful resource when it comes to conducting the bioinformatics myself"

  • R for beginners – An introduction course 21st-23rd November 2018

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    Centre for Genomic Research and Computational Biology Facility, University of Liverpool 

    This 3-day R course is presented by the Computational Biology Facility (CBF) and the Centre for Genomic Research (CGR) and partially funded by the Technology Directorate at the University of Liverpool. It primarily focuses on the basis of R language and introduction to visualisation and statistics analyses.The course is designed to introduce R from the very basics. Therefore applicants do not need any prior experience to attend the workshop, just the desire and need to learn R.
     
     

    Feedbacks from participants:

    "One to one help when needed, easy to follow instructions"

    "The content of the handouts will be very useful for the future and the level was perfect, exactly what was expected"

  • NERC Metagenomics Course 18th-20th July 2018

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    Centre for Genomic Research, University of Liverpool

     
    This 3-day bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

    16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 3-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

    • Sequence data QC and preparation for downstream analyses
    • Metagenomic shotgun sequence analysis.
    • Taxonomic profiling (MetaPhlAn)
    • Metagenome assembly (MEGAHIT) and annotation (Prokka)
    • Functional annotation (Cognizer)
    • Data visualisation
    • Analysis of 16S rRNA data with QIIME
    • Laboratory tour of sequencing laboratory
    • Metagenome functional prediction using metagenetic data

     

    Feedbacks from partecipants:

    "It was great learning from trainers who are experts in the field"

    "The course was well structured with the information given in the the talks relevant to the next practical session. It was useful to learn the theory behind each step in the analysis and the have the opportunity to perform the analysis in the practicals".

     

  • Gene Expression Workshop 14th-16th May 2018

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    Centre for Genomic Research, University of Liverpool

    The course is presented by the Centre for Genomic Research and the Computational Biology Facillity at the University of Liverpool. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

    This course is designed to provide a 2.5-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. Whole transcriptome profiling is now well established, and can be applied to a wide range of biological questions. However, it is challenging both in handling the huge amounts of data generated, and downstream interpretation.

    This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

    • Introduction to next-generation sequencing, sequencing QC and RNA-Seq
    • Experimental design and cost implications
    • Laboratory tour of sequencing laboratory
    • Mapping and visualising RNAseq data
    • Multi-omics data integration

     

  • NERC Metagenomics Course 25th-27th April 2018

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    Centre for Genomic Research, University of Liverpool

    This 3-day bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

    16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 3-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

    • Sequence data QC and preparation for downstream analyses
    • Metagenomic shotgun sequence analysis.
    • Taxonomic profiling (MetaPhlAn)
    • Metagenome assembly (MEGAHIT) and annotation (Prokka)
    • Functional annotation (Cognizer)
    • Data visualisation
    • Analysis of 16S rRNA data with QIIME
    • Laboratory tour of sequencing laboratory
    • Metagenome functional prediction using metagenetic data

     

  • NERC Metagenomics Course 29th-30th June 2017

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    Centre for Genomic Research, University of Liverpool

    This bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

    The 16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 2-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

    • Introduction to Unix and the command line.
    • Sequence data QC and preparation for downstream analyses
    • Metagenomic shotgun sequence analysis.
    • Taxonomic profiling (MetaPhlAn)
    • Metagenome assembly (MEGAHIT) and annotation (Prokka)
    • Functional annotation (Cognizer)
    • Data visualisation
    • Analysis of 16S rRNA data with QIIME
  • Gene Expression Workshop 10th-12st April 2017

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    Centre for Genomic Research, University of Liverpool 

    The course is presented by the Centre for Genomic Research and the Centre for Computational Biology and Modeling at the University of Liverpool. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

    This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. Whole transcriptome profiling in now well established, and can be applied to a wide range of biological questions. However, it is challenging both in handling the huge amounts of data generated, and downstream interpretation.

    This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

    • Introduction to next-generation sequencing and RNA-Seq
    • Experimental design and cost implications
    • Laboratory tour of sequencing laboratory
    • Informatic issues: The command-line interface, Data handling and statistical analyses, Analysis in the iPlant environment, Network modelling
  • Metagenomics Workshop 23nd -24rd March 2017

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    Centre for Genomic Research, University of Liverpool 

    This bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

    The 16S rRNA gene profiling (metagenetics) and shotgun sequence based metagenomics are now well established and can be utilised to characterise complex populations. The course will provide a 2-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

    • Introduction to Unix and the command line.
    • Sequence data QC and preparation for downstream analyses
    • Metagenomic shotgun sequence analysis.
    • Taxonomic profiling (MetaPhlAn)
    • Metagenome assembly (MEGAHIT) and annotation (Prokka)
    • Functional annotation (Cognizer)
    • Data visualisation
    • Analysis of 16S rRNA data with QIIME
  • Microbiome study design and analysis 21st – 24th March 2017

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    University of Malawi, College of Medicine

    (Sponsored by the BBSRC IAA award to FHLS)

  • Investigating population diversity in Brachiaria 5th – 11th March 2017

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    ILRI Kenia

    (Sponsored by the BBSRC IAA award to FHLS)

  • Working with Parasite Database Resources (Wellcome Trust Advanced Courses program) 16th – 21st October 2016

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    Working with Parasite Database Resources (Wellcome Trust Advanced Courses program) 16th – 21st October 2016

    Institute of Hygiene, Montevideo, Uruguay

  • Gene Expression Workshop 29th March-1st April 2016

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    Centre for Genomic Research, University of Liverpool  

    The course is presented by the Centre for Genomic Research at the University of Liverpool and sponsored by the Physiological Society. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

    This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

    This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

    • Designing a RNAseq gene expression experiment
    • Quality control and library preparation
    • Introduction to CyVerse: Data preparation and analysis
    • Laboratory tour of sequencing laboratory
    • Informatic issues: The command-line interface, Data handling and statistical analyses, Analysis in the iPlant environment, Network modelling
  • Working with Parasite Database Resources (Wellcome Trust Advanced Courses program) 18th – 23rd October 2015

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    Hinxton, Cambridgeshire

  • Metagenomics Workshop 22nd March - 23rd March 2016

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    Centre for Genomic Research, University of Liverpool

    This bioinformatics course is presented by the Centre for Genomic Research and funded by the Natural Environment Research Council (NERC). It primarily focuses on practical computer sessions designed to provide delegates with hands-on experience of the informatics involved in analysing metagenomic and metagenetic datasets.

    The course will provide a 2-day introduction to the conceptual and practical issues involved in analysing such datasets, generated from the Illumina NGS platforms, and comprises the following sessions:

    • Introduction to shotgun metagenomic sequence analysis
    • Sequence data QC and preparation for downstream analyses
    • Analysis of 16S rRNA data with QIIME
  • Gene Expression Workshop 30th March – 2nd April 2015

    open-content-icon

    Centre for Genomic Research, University of Liverpool 

    The course is presented by the Centre for Genomic Research at the University of Liverpool and funded by the Physiological Society and Natural Environment Research Council (NERC). We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

    This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

    This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

    • Introduction to next generation sequencing and RNAseq
    • Designing a gene expression experiment, microarray and RNAseq
    • Transcriptome and genome assembly and gene annotation
    • Quality control and library preparation 
    • Reverse engineering biological pathways from observational data
    • Informatic issues: The command-line interface, Data handling and statistical analyses, Network modelling
  • Software Carpentry Bootcamp 17th - 18th November 2014

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    GARNet and Centre for Genomic Research at the University of Liverpool

    Software Carpentry teaches principles of good programming applicable to any coding language or application, whether sequencing data, phenotypic trait analysis or biochemical assays. Tutorials will start from first principles and cover Python programming, managing data in Excel and Python; and scientific plotting using BioPython and R. Teaching will be a combination of live coding guided by the trainer and independent practical exercises.

    Introducing biologists to:

    • Git and GitHub
    • Python programming
    • Version control
    • Good practice and test-driven development 
    • Applying data managment aand scientific programming to your project.
  • Gene Expression Workshop 7th-11th April 2014

    open-content-icon

    Centre for Genomic Research, University of Liverpool 

    The course is presented by the Centre for Genomic Research at the University of Liverpool and funded by the Physiological Society. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

    This course is designed to provide a 5-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

    This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

    • Introduction to next generation sequencing and RNAseq
    • Designing a gene expression experiment, microarray and RNAseq
    • Transcriptome and genome assembly and gene annotation
    • Quality control and library preparation 
    • Mapping and visualizing RNAseq data
    • Reverse engineering biological pathways from observational data
    • Informatic issues: The command-line interface, Data handling and statistical analyses, Network modelling
  • CGR Advanced Course in Genome-wide Gene Expression Profiling by Array and NextGen Sequencing 21st – 24th January 2013

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    Centre for Genomic Research, University of Liverpool 

    The course is presented by the Centre for Genomic Research at the University of Liverpool and funded by the Physiological Society and in collaboration with the University of Sheffield. We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

    This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

    This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

    • Advantages of nextgeneration sequencing over microarrays – gene discovery, transcriptome discovery
    • Quality control and library preparation 
    • Designing a gene expression experiment, microarray and RNAseq
    • The experiment - design and cost implications
    • Installation and implementation of informatic and analytical software
    • Introduction to high-throughput sequencing data analysis
    • Reverse engineering gene networks – systems approaches
    • Introduction to functional analysis
  • CGR Advanced Course in Genome-wide Gene Expression Profiling by Microarrays and Next Generation Sequencing 10th-13th October 2011

    open-content-icon

    Centre for Genomic Research, University of Liverpool 

    The course is presented by the Centre for Genomic Research at the University of Liverpool in collaboration with the University of Sheffield and funded by the Physiological Society.

    We offer keynote talks by experts in the areas covered and a large portion of the course comprises practical computer sessions, allowing delegates to obtain hands-on experience.

    This course is designed to provide a 4-day introduction to the conceptual, practical and interpretational issues involved in large-scale gene expression profiling. 

    This course covers aspects associated with next-generation sequencing-based approaches to transcriptional profiling (RNA-Seq), comprising the following sections:

    • Opportunities presented by genome-wide expression profiling
    • Microarray technologies based on cDNA and oligonucleotides
    • Sequencing-based approaches to transcript abundance
    • Designing a gene expression experiment, microarray and RNAseq
    • Analysis of Affymetrix microarray data
    • Enrichment analysis of pathways and process