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16 events found

Organizer: University of Cambridge  or Australian BioCommons 

  • WORKSHOP: Single cell RNAseq analysis in R

    22 - 23 August 2022

    WORKSHOP: Single cell RNAseq analysis in R http://tess.elixir-uk.org/events/workshop-single-cell-rnaseq-analysis-in-r Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using[ Seurat](https://satijalab.org/seurat/index.html) - an R package for QC, analysis, and exploration of single-cell RNAseq data. We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data. **Lead trainers:** Dr Sarah Williams, Senior Bioinformatician, QCIF Mr Nick Matigan, Biostatistician and Bioinformatician, QCIF Dr Ahmed Mehdi, Senior Biostatistician, QCIF **Format** This online workshop will take place over two half-day sessions. You must attend both sessions. Expert trainers will guide you through each of the topics and provide activities to help you put your new skills into action. **Date/Time:** 22 and 23 August 2022, 1-5pm AEST/ ACST/AWST **Location:** Online **Learning outcomes:** By the end of the workshop you should be able to: 1. Load gene counts into a Seurat format 2. Perform QC and select cells for further analysis 3. Filter and normalise scRNAseq data 4. Cluster cells and identify cluster markers 5. Visualise scRNAseq expression data **Who the workshop is for:** This workshop is for Australian researchers who have or will work on scRNAseq data as part of their projects. You must be associated with an Australian organisation for your application to be considered. This workshop will not teach you the basics of R. While you don’t need to be an expert, you require some basic familiarity with R. For example you should be able to work with tables of data, know how to load an R package, make basic plots (ideally with ggplot2). You should also have basic knowledge of single cell RNA sequencing technology. **How to apply:** This workshop is free but participation is subject to application with selection. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. Applications close at **11:59pm AEDT, Wednesday 10 August 2022**. **[Apply here](https://biocommons-scrnaseq.eventbrite.com.au/)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/) and[ Queensland Cyber Infrastructure Foundation (QCIF)](https://www.qcif.edu.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative)._ _This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons_ 2022-08-22 13:00:00 UTC 2022-08-23 17:00:00 UTC Australian BioCommons RNA-Seq Australian Biocommons training@biocommons.org.au [] [] 80 workshops_and_courses registration_of_interest Single Cell technologiesscRNAseqSeuratR software
  • WEBINAR: Getting started with whole genome mapping and variant calling on the command line

    24 August 2022

    WEBINAR: Getting started with whole genome mapping and variant calling on the command line http://tess.elixir-uk.org/events/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are. In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need. **Who the webinar is for** This webinar is intended for life scientists who are using and building whole genome sequencing mapping and variant calling pipelines. Some familiarity with the concepts of whole genome sequencing is recommended. **Presenter:** Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney **Date/time:** 24 August 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here] (https://unimelb.zoom.us/webinar/register/WN_ekHib2_2QYazaH06VFMPgQ)** 2022-08-24 12:00:00 UTC 2022-08-24 13:00:00 UTC Australian BioCommons Whole genome sequencing Sequencing Genomics Bioinformatics Workflows Australian Biocommons training@biocommons.org.au [] [] 500 workshops_and_courses first_come_first_served []
  • Introduction to Python for Biologists (ONLINE LIVE TRAINING)

    12 - 19 September 2022

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Python for Biologists (ONLINE LIVE TRAINING) http://tess.elixir-uk.org/events/introduction-to-python-for-biologists-online-live-training-39cbbce2-9546-4bbe-a980-e258b1c222f5 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=4372976&course-title=Introduction%20to%20Python%20for%20Biologists).'' 2022-09-12 08:30:00 UTC 2022-09-19 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Python script 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
  • Analysis of single cell RNA-seq data (IN PERSON)

    12 - 26 September 2022

    Cambridge, United Kingdom

    Elixir node event
    Analysis of single cell RNA-seq data (IN PERSON) http://tess.elixir-uk.org/events/analysis-of-single-cell-rna-seq-data-in-person Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging. In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq. 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 account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4371238&&course-title=Analysis%20of%20single%20cell%20RNA-seq%20data).'' 2022-09-12 08:30:00 UTC 2022-09-26 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Transcriptomics Functional genomics Data visualisation Data mining 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 (IN PERSON)

    13 - 14 September 2022

    Cambridge, United Kingdom

    Elixir node event
    Introduction to R for Biologists (IN PERSON) http://tess.elixir-uk.org/events/introduction-to-r-for-biologists-in-person PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click [here.](https://training.csx.cam.ac.uk/bioinformatics/event/4372955) 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. 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 account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4376515&course-title=Introduction%20to%20R%20for%20Biologists).'' 2022-09-13 08:30:00 UTC 2022-09-14 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
  • Introduction to R for Biologists (ONLINE)

    13 - 14 September 2022

    Cambridge, United Kingdom

    Elixir node event
    Introduction to R for Biologists (ONLINE) http://tess.elixir-uk.org/events/introduction-to-r-for-biologists-online PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click [here.](https://training.csx.cam.ac.uk/bioinformatics/event/4376515) 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 account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4372955&course-title=Introduction%20to%20R%20for%20Biologists).'' 2022-09-13 08:30:00 UTC 2022-09-14 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
  • Using the Ensembl Genome Browser (IN PERSON)

    15 September 2022

    Cambridge, United Kingdom

    Elixir node event
    Using the Ensembl Genome Browser (IN PERSON) http://tess.elixir-uk.org/events/using-the-ensembl-genome-browser-in-person 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=4379129&course-title=Using%20the%20Ensembl%20Genome%20Browser).'' 2022-09-15 08:30:00 UTC 2022-09-15 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
  • Ensembl REST API workshop (IN PERSON)

    16 September 2022

    Cambridge, United Kingdom

    Elixir node event
    Ensembl REST API workshop (IN PERSON) http://tess.elixir-uk.org/events/ensembl-rest-api-workshop-in-person 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=4379159&course-title=Ensembl%20REST%20API%20Workshop).'' 2022-09-16 08:30:00 UTC 2022-09-16 15:30:00 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
  • WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud

    20 September 2022

    WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud http://tess.elixir-uk.org/events/webinar-portable-reproducible-and-scalable-bioinformatics-workflows-using-nextflow-and-pawsey-nimbus-cloud Bioinformatics workflows can support portable, reproducible and scalable analysis of omics datasets but using workflows can be challenging for both beginners and experienced bioinformaticians. Beginners face a steep learning curve to be able to build and deploy their own bioinformatics workflows while those with more experience face challenges productionising and scaling code for custom workflows and big data. Bioinformaticians across the world are using Nextflow to build and manage workflows. Many of these workflows are shared for others to use and supported by the community via [nf-co.re](https://nf-co.re/). So far, [39 workflows for omics data](https://nf-co.re/pipelines) are available with another 23 under development. These workflows cover common analyses such as RNAseq, mapping, variant calling, single cell transcriptomics and more and can be easily deployed by anyone, regardless of skill level. In this webinar, Nandan Deshpande from the Sydney Informatics Hub, University of Sydney, will discuss how you can deploy freely available Nextflow (nf.co-re) bioinformatics workflows with a single command. We describe how you can quickly get started deploying these workflows using Pawsey Nimbus Cloud. For advanced users, we show you how you can use Nextflow to build your own workflows that save you time and support reproducible, portable and scalable analysis. In the latter half of the webinar, Sarah Beecroft from the Pawsey Supercomputing Research Centre will talk about their Nimbus Cloud systems. While Nextflow supports portability and can run on many computing infrastructures, we describe why we specifically love using Nimbus with Nextflow for many bioinformatics projects. We will describe some of the nf.co-re workflows that we have used on Nimbus and the research outcomes. We will also cover when not to use Nimbus and the alternatives we recommend. **Speakers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Sarah Beecroft, Bioinformatics Applications Specialist, Pawsey Supercomputing Research Centre. **Who the webinar is for:** This webinar is for biologists who are new to bioinformatics on the command-line and bioinformaticians and would like to use existing best practice workflows available through nf.co-re. **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here](https://unimelb.zoom.us/webinar/register/WN_P54j05SaQ6qbQz8h0Su_Zw)** 2022-09-20 12:00:00 UTC 2022-09-20 13:00:00 UTC Australian BioCommons Workflows Bioinformatics Australian Biocommons training@biocommons.org.au [] [] 500 workshops_and_courses first_come_first_served Nextflownf-coreWorkflowsBioinformaticsReproducibility
  • WORKSHOP: RNA-Seq: reads to differential genes and pathways

    27 September 2022

    WORKSHOP: RNA-Seq: reads to differential genes and pathways http://tess.elixir-uk.org/events/workshop-rna-seq-reads-to-differential-genes-and-pathways RNA sequencing (RNA-seq) is a common method used to understand the differences in gene expression and molecular pathways between two or more groups. This workshop introduces the fundamental concepts of RNA sequencing experiments and will allow you to try out the analysis using data from a study of Williams-Beuren Syndrome, a rare disease. In the first part of the workshop you will learn how to convert sequence reads into analysis ready count data. To do this we will use[ nf-core/rnaseq](https://nf-co.re/rnaseq/usage) - a portable, scalable, reproducible and publicly available workflow on[ Pawsey Nimbus Cloud](https://pawsey.org.au/systems/nimbus-cloud-service/). In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis! **Lead Trainers:** Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub **Date/Time**: 27 & 28 September 2022, 2-5pm AEST/1:30-4:30pm ACST/12-3pm AWST **Format:** This online workshop will take place over two three-hour sessions. You must attend both sessions in order to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action. **Learning outcomes:** By the end of the workshop you should be able to: 1. List the steps involved in analysis of RNA-seq data 2. Describe key concepts and considerations for RNA-seq experiments 3. Describe the benefits of using nf-core workflows 4. Deploy an RNA-seq nf-core workflow on Pawsey’s Nimbus Cloud to perform: 1. Quality control 2. Alignment 3. Quantification to generate raw counts 5. Use R/RStudio on Pawsey’s Nimbus Cloud to perform 4. Quality control 5. Identify differentially expressed genes using DESeq2 6. Perform functional enrichment/pathway analysis **Who the workshop is for:** This workshop is for Australian researchers who have or will work on RNAseq data as part of their projects. You must be associated with an Australian organisation for your application to be considered. The workshop will be conducted in a Unix environment and will use R/RStudio. Basic command line knowledge is required. You must know how to navigate the directory structure and copy files between the computers. If you need a refresher on Unix/Linux try[ this online tutorial](https://linuxjourney.com/lesson/the-shell). Basic knowledge of R/RStudio is required. You must know how to set up directories, run commands, reading in and outputting files. If you need a refresher on R/RStudio try the[ Introduction to R and RStudio section](https://swcarpentry.github.io/r-novice-gapminder/01-rstudio-intro/index.html) of this online tutorial. It’s recommended that you watch the webinar[ Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](http://biocommons.org.au/events/nextflow-nimbus) in advance. You may join this webinar live on 20 September 2022. A recording will be posted on the[ Australian BioCommons YouTube Channel](https://www.youtube.com/c/AustralianBioCommonsChannel). **How to apply:** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST, Sunday 11 September 2022**. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. **[Apply here](https://biocommons-rnaseq-2022.eventbrite.com.au/)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/), Sydney Informatics Hub and Pawsey Supercomputing Research Centre with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative)._ _This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons_ 2022-09-27 14:00:00 UTC 2022-09-27 17:00:00 UTC Australian BioCommons RNA-Seq Workflows Gene expression Functional genomics Bioinformatics Australian Biocommons training@biocommons.org.au [] [] 100 workshops_and_courses registration_of_interest BioinformaticsRNA-seqGene ExpressionPathway analysisNextflownf-coreWorkflowsFunctional analysis
  • Core Statistics using R (ONLINE)

    28 - 30 September 2022

    Cambridge, United Kingdom

    Elixir node event
    Core Statistics using R (ONLINE) http://tess.elixir-uk.org/events/core-statistics-using-r-online PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click [here.](https://training.csx.cam.ac.uk/bioinformatics/event/4373318) This [award winning](https://www.cctl.cam.ac.uk/teaching-prizes/tel-prize/2020) virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course: # Use R confidently for statistics and data analysis # Be able to analyse datasets using standard statistical techniques # Know which tests are and are not appropriate R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4373279&course-title=Core%20Statistics%20using%20R).'' 2022-09-28 08:30:00 UTC 2022-09-30 16:00:00 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 individualsThis course is included as part of several DTP and MPhil programmesas well as other departmental training within the University of Cambridge (potentially under a different name) so participants who have attended statistics training elsewhere should check before applying. workshops_and_courses [] HDRUK
  • Core Statistics using R (IN PERSON)

    28 - 30 September 2022

    Cambridge, United Kingdom

    Elixir node event
    Core Statistics using R (IN PERSON) http://tess.elixir-uk.org/events/core-statistics-using-r-in-person PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click [here.](https://training.csx.cam.ac.uk/bioinformatics/event/4373279) This [award winning](https://www.cctl.cam.ac.uk/teaching-prizes/tel-prize/2020) virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course: # Use R confidently for statistics and data analysis # Be able to analyse datasets using standard statistical techniques # Know which tests are and are not appropriate R is an open source programming language so all of the software we will use in the course is free. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. 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 account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4373318&course-title=Core%20Statistics%20using%20R).'' 2022-09-28 08:30:00 UTC 2022-09-30 16:00:00 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 individualsThis course is included as part of several DTP and MPhil programmesas well as other departmental training within the University of Cambridge (potentially under a different name) so participants who have attended statistics training elsewhere should check before applying. workshops_and_courses [] HDRUK
  • Introduction to working with UNIX and bash (ONLINE LIVE TRAINING)

    19 - 20 October 2022

    Cambridge, United Kingdom

    Elixir node event
    Introduction to working with UNIX and bash (ONLINE LIVE TRAINING) http://tess.elixir-uk.org/events/introduction-to-working-with-unix-and-bash-online-live-training-25ff634e-07af-4a19-9909-85054bb3b920 Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands. Building on the techniques learnt so far, we will then construct bash scripts combining the commands and structures already learnt into more complex, reusable tools. We will look at how we can apply these scripts to common problems faced in UNIX environments such as: communicating with remote servers; managing custom software installations and integrating these tools into our simple pipelines. This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4373475&course-title=Introduction%20to%20working%20with%20Unix%20and%20bash).'' 2022-10-19 08:30:00 UTC 2022-10-20 12:00:00 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
  • Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING)

    18 November - 2 December 2022

    Cambridge, United Kingdom

    Elixir node event
    Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) http://tess.elixir-uk.org/events/analysis-of-bulk-rna-seq-data-online-live-training-87c663c9-a872-4312-ba6c-7fd5c3034ebc 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=4373564&course-title=Analysis%20of%20bulk%20RNA-seq%20data).'' 2022-11-18 09:30:00 UTC 2022-12-02 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR 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
  • Reproducible Research with R (IN PERSON)

    1 December 2022

    Cambridge, United Kingdom

    Elixir node event
    Reproducible Research with R (IN PERSON) http://tess.elixir-uk.org/events/reproducible-research-with-r-in-person PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click [here.](https://training.csx.cam.ac.uk/bioinformatics/event/4373728) This course introduces concepts about reproducibility that can be used when you are programming in R. We will explore how to create notebooks - a way to integrate your R analyses into reports using Rmarkdown. The course also introduces the concept of version control. We will learn how to create a repository on GitHub and how to work together on the same project collaboratively without creating conflicting versions of files. 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 account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4377410&course-title=Reproducible%20Research%20with%20R).'' 2022-12-01 09:30:00 UTC 2022-12-01 17:00:00 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
  • Reproducible Research with R (ONLINE)

    1 December 2022

    Cambridge, United Kingdom

    Elixir node event
    Reproducible Research with R (ONLINE) http://tess.elixir-uk.org/events/reproducible-research-with-r-online PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click [here.](https://training.csx.cam.ac.uk/bioinformatics/event/4377410) This course introduces concepts about reproducibility that can be used when you are programming in R. We will explore how to create notebooks - a way to integrate your R analyses into reports using Rmarkdown. The course also introduces the concept of version control. We will learn how to create a repository on GitHub and how to work together on the same project collaboratively without creating conflicting versions of files. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4373728&course-title=Reproducible%20Research%20with%20R).'' 2022-12-01 09:30:00 UTC 2022-12-01 17:00:00 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

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