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24 events found

Content provider: VIB Bioinformatics Core  or NBIS 

  • Basic statistics in R, Ghent

    15 - 29 January 2019

    Ghent, Belgium

    Elixir node event
    Basic statistics in R, Ghent https://tess.elixir-europe.org/events/basic-statistics-in-r-ghent b'\nGet an idea of what R and Rstudio is\r\nUse R to handle data: creating, reading, reformatting and writing data\r\nUse R to create graphics\r\nUse basic statistical techniques in R : normality tests, t-tests, wilcoxon tests, chi square tests, correlations, survival analysis...\r\nWrite and use R scripts\n\r\n\n \nThis training gives an introduction to the use of the statistical software language R. R is a language for data analysis and graphics. This introduction to R is aimed at beginners. The training covers data handling, graphics, and basic statistical techniques. \r\nR is for free and for more information you can visit the site the CRAN web site.This training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents). A full overview of statistical analyses in R including regression, ANOVA will be given in the follow-up training Basic statistics in R, part II.\n\r\n \r\nRequirements\r\nThe training is intended for people who have no experience with R. However, understanding of basic statistical concepts is required, such as data types, normal distribution, descriptive statistics, tests for comparing groups... If you don\'t have sufficient statistical background you are strongly encouraged to attend the Basic statistics theorytraining. \r\nThis training is recommended for people with no experience in R who are planning to follow a training that requires some R background, like the mass spectrometry , the single cell RNA-Seq and the bulk RNA-Seq training....\n\r\n\n' 2019-01-15 09:30:00 UTC 2019-01-29 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Ghent, Belgium Bio-Accelerator Ghent Belgium 9052 [] [] [] [] [] []
  • VIB Interest Group Meeting - containers and workflows

    25 January 2019

    Gent, Belgium

    Elixir node event
    VIB Interest Group Meeting - containers and workflows https://tess.elixir-europe.org/events/vib-interest-group-meeting-containers-and-workflows 2019-01-25 09:30:00 UTC 2019-01-25 16:30:00 UTC VIB Bioinformatics Core Clemenspoort - zaal Seelos, Gent, Belgium Clemenspoort - zaal Seelos Gent Belgium 9000 [] [] [] [] [] []
  • Course: single-cell RNA sequencing data analysis

    4 - 7 February 2019

    Elixir node event
    Course: single-cell RNA sequencing data analysis https://tess.elixir-europe.org/events/course-single-cell-rna-sequencing-data-analysis Course name: Single cell RNA sequencing data analysis Course dates: 2019-02-04 to 2019-02-06 Course location: SciLifeLab, Tomtebodavägen 23A, 171 65 Solna National course open for PhD students, postdocs, researchers and other employees in need of single cell RNA-seq data analysis skills within all Swedish universities Important dates Application opens: December 10 2018 Application closes: January 20 Confirmation to accepted students: January 22 Responsible teachers: Åsa Björklund If you do not receive information according to the above dates please contact: asa.bjorklund@scilifelab.se Course fee A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and course dinner.. *Please note that NBIS cannot invoice individuals Course content This course will cover the basic steps in single cell RNAseq (scRNAseq) processing and data analysis. Topics covered will include: ● An overview of the current scRNAseq techniques ● Basic overview of pipelines for processing raw reads into expression values ● Quality control of scRNAseq data ● Dimensionality reduction and clustering techniques ● Data normalization ● Differential gene expression for scRNAseq data ● Examples on how to use these tools in a research project. Entry requirements Required for being able to follow the course and complete the computer exercises ● Basic knowledge in Linux is a requirement. We will not teach Linux at the course and you may have considerable trouble to follow the practical sessions if you are not reasonably used to work in a Linux environment. ● Be able to bring your own laptop with R installed for the practical computational exercises. Instructions on installation will be sent by email to accepted participants. ● Some programming/scripting experience is required (preferably in R). Desirable: ● Experience working on the SNIC center Uppmax is desirable, but not required. We encourage accepted participants to do an Uppmax tutorial before the course. ● Previous experience with RNA-seq analysis and/or participation in NGS/RNA-seq course is an advantage. Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Link to application: https://goo.gl/forms/0x9ssllId5Jxn9dB3 2019-02-04 09:00:00 UTC 2019-02-07 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Course: Introduction to Bioinformatics using NGS data

    4 - 9 February 2019

    Elixir node event
    Course: Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/course-introduction-to-bioinformatics-using-ngs-data https://www.scilifelab.se/events/introduction-to-bioinformatics-using-ngs-data-uppsala/ 2019-02-04 09:00:00 UTC 2019-02-09 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Analysis of single cell RNA-Seq data from 10x Genomics

    4 - 5 February 2019

    Ghent, Belgium

    Elixir node event
    Analysis of single cell RNA-Seq data from 10x Genomics https://tess.elixir-europe.org/events/analysis-of-single-cell-rna-seq-data-from-10x-genomics 2019-02-04 09:30:00 UTC 2019-02-05 17:00:00 UTC VIB Bioinformatics Core iGent Tower, Ghent, Belgium iGent Tower Ghent Belgium 9052 [] [] [] [] [] []
  • RNA-Seq analysis for differential expression

    11 - 18 February 2019

    Leuven, Belgium

    Elixir node event
    RNA-Seq analysis for differential expression https://tess.elixir-europe.org/events/rna-seq-analysis-for-differential-expression-in-genepattern b'You will execute a complete analysis workflow in GenePattern, Galaxy or command line and R to detect differential expression between two conditions\n\r\n\r\n\n We\'ll go through the different steps of the workflow:\r\n\n \nQuality control of the sequence reads to detect biases or contaminating adapters.\r\nMapping of the reads to the reference genome with use of a transcript database model.\r\nQuality control  of the mapping results.\r\nAdjusting the mapping data to compensate for artefacts like duplicates.\r\nCalculate transcript counts usable for differential expression and merging of count tables \n\r\nComputing differential expression using  DESeq2.\n\r\n\r\n\n • fastQC • trimmomatic• Groomer • STAR• samtools• Picard • RSeQC• HTSeq• R - RStudio - Bioconductor - various packages \n\r\n\r\n\n  \r\nFamiliarity with \n \nRNA-seq assembly\r\nRNA-seq analysis for isoform detection\r\nRNA-seq analysis for detection of short RNA species\n\r\n\n \n.Organised by the VIB Bioinformatics Core​\n\r\n\n' 2019-02-11 09:30:00 UTC 2019-02-18 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • RNA-Seq analysis for differential expression, extra session

    12 - 25 February 2019

    Leuven, Belgium

    Elixir node event
    RNA-Seq analysis for differential expression, extra session https://tess.elixir-europe.org/events/rna-seq-analysis-for-differential-expression-extra-session b'You will execute a complete analysis workflow in GenePattern, Galaxy or command line and R to detect differential expression between two conditions\n\r\n\n We\'ll go through the different steps of the workflow:\r\n\n \nQuality control of the sequence reads to detect biases or contaminating adapters.\r\nMapping of the reads to the reference genome with use of a transcript database model.\r\nQuality control  of the mapping results.\r\nAdjusting the mapping data to compensate for artefacts like duplicates.\r\nCalculate transcript counts usable for differential expression and merging of count tables \n\r\nComputing differential expression using  DESeq2.\n\r\n\n • fastQC • trimmomatic• Groomer • STAR• samtools• Picard • RSeQC• HTSeq• R - RStudio - Bioconductor - various packages \n\r\n\n  \r\nFamiliarity with \n \nRNA-seq assembly\r\nRNA-seq analysis for isoform detection\r\nRNA-seq analysis for detection of short RNA species\n\r\n\n \n.Organised by the VIB Bioinformatics Core​\n\r\n​\n' 2019-02-12 09:30:00 UTC 2019-02-25 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Basic statistics theory

    22 February 2019

    Leuven, Belgium

    Elixir node event
    Basic statistics theory https://tess.elixir-europe.org/events/basic-statistics-theory b'After this basic statistics theory session, you should be able to:\r\nUnderstand basic statistical concepts and methods for statistical analysis of life sciences data\r\n\r\nChoose the correct statistical test for analyzing your data\n\r\n\n This training gives an introduction to the use of statistics for basic analyses of life sciences data. This training is a prerequisite introduction to a series of \r\nhands-on trainings on the statistical analysis of life sciences data: \r\n\'Basic statistics in R\' and \'Basic statistics in Graphpad Prism\'.\r\n If you want to follow one of these trainings, you have to follow this \r\nintroduction. Ít will give you all the theoretical background that you need. Those that already have a strong statistical background may register directly for the \'Basic statistics in R, part II\' training. \n\r\n\r\n\r\n\n No skills required. \n\r\n\n  9h30-12h30: Theoretical background\r\n\n' 2019-02-22 09:30:00 UTC 2019-02-22 16:30:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Analyzing flow cytometry data in FlowJo

    25 February 2019

    Ghent (Sint-Denijs-Westrem), Belgium

    Elixir node event
    Analyzing flow cytometry data in FlowJo https://tess.elixir-europe.org/events/analyzing-flow-cytometry-data-in-flowjo b'Learn researchers how to analyze flow cytometry data in an efficient way using FlowJo v10,the world’s nr.1 analysis software tool for flow cytometry data.\r\n\n FlowJo version10 is a newly designed version of the famous FlowJo software. In contrast with previous versions (iOS only), version 10 is now a multi-platform software tool (Windows, iOS, Linux). It now has a very intuitive user interface designed to analyze your data in a very practical and fast way.\r\n\n Prior knowledge in general flow cytometry is required but the general principles will be repeated\r\n\n' 2019-02-25 09:30:00 UTC 2019-02-25 17:00:00 UTC VIB Bioinformatics Core Holiday Inn Gent Expo, Ghent (Sint-Denijs-Westrem), Belgium Holiday Inn Gent Expo Ghent (Sint-Denijs-Westrem) Belgium 9051 [] [] [] [] [] []
  • Advanced FlowJo training

    26 February 2019

    Gent (Sint-Denijs-Westrem), Belgium

    Elixir node event
    Advanced FlowJo training https://tess.elixir-europe.org/events/advanced-flowjo-training b'\nParticipants must have experience with FlowJo. If you\'re new to the software you can attend our FlowJo introduction training​ first. ​\r\n\n \r\n\r\n\n' 2019-02-26 09:30:00 UTC 2019-02-26 17:00:00 UTC VIB Bioinformatics Core Holiday Inn Ghent Expo, Gent (Sint-Denijs-Westrem), Belgium Holiday Inn Ghent Expo Gent (Sint-Denijs-Westrem) Belgium 9051 [] [] [] [] [] []
  • Basic statistics in R

    11 - 18 March 2019

    GENT, Belgium

    Elixir node event
    Basic statistics in R https://tess.elixir-europe.org/events/basic-statistics-in-r b'\n\nGet an idea of what R and Rstudio is\r\nUse R to handle data: creating, reading, reformatting and writing data\r\nUse R to create graphics\r\nUse basic statistical techniques in R : normality tests, t-tests, wilcoxon tests, chi square tests, correlations, survival analysis...\r\nWrite and use R scripts\n\r\n\r\n\n \nThis training gives an introduction to the use of the statistical software language R. R is a language for data analysis and graphics. This introduction to R is aimed at beginners. The training covers data handling, graphics, and basic statistical techniques. \r\nR is for free and for more information you can visit the site the CRAN web site.This\r\n training is an introduction to the use of R and RStudio and stops at very basic \r\nanalyses (t-tests and non-parametric equivalents). A full overview of statistical analyses in R including regression, \r\nANOVA will be given in the follow-up training Basic statistics in R, part II.\n\r\n \r\nRequirements\r\nThe training is intended for people who have no experience with R. However, understanding of basic statistical concepts is required, such as data types, normal distribution, descriptive statistics, tests for comparing groups... If you don\'t have sufficient statistical background you are strongly encouraged to attend the Basic statistics theory training. \r\nThis training is recommended for people with no experience in R who are planning to follow a training that requires some R background, like the mass spectrometry training, the single cell RNA-Seq and the bulk RNA-Seq training....\n\r\n\n' 2019-03-11 09:30:00 UTC 2019-03-18 17:00:00 UTC VIB Bioinformatics Core Clemenspoort, GENT, Belgium Clemenspoort GENT Belgium 9000 [] [] [] [] [] []
  • Carpentries Instructor Training course/event (Elixir)

    3 - 5 April 2019

    Elixir node event
    Carpentries Instructor Training course/event (Elixir) https://tess.elixir-europe.org/events/carpentries-instructor-training-course-event-elixir Room Air/Fire Web page Carpentries Instructor Training Course: https://carpentries.github.io/instructor-training/ 2019-04-03 09:00:00 UTC 2019-04-05 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Using MOFA for integration of omics data

    3 May 2019

    Leuven, Belgium

    Elixir node event
    Using MOFA for integration of omics data https://tess.elixir-europe.org/events/using-mofa-for-integration-of-omics-data 2019-05-03 09:30:00 UTC 2019-05-03 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Course: Genome Annotation

    6 - 9 May 2019

    Elixir node event
    Course: Genome Annotation https://tess.elixir-europe.org/events/course-genome-annotation More information will follow 2019-05-06 09:00:00 UTC 2019-05-09 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Course: RNAseq

    13 - 16 May 2019

    Elixir node event
    Course: RNAseq https://tess.elixir-europe.org/events/course-rnaseq More information will follow 2019-05-13 09:00:00 UTC 2019-05-16 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Course: Quick and clean - advanced python for data science in Biology

    20 - 25 May 2019

    Elixir node event
    Course: Quick and clean - advanced python for data science in Biology https://tess.elixir-europe.org/events/course-quick-and-clean-advanced-python-for-data-science-in-biology More information will follow 2019-05-20 09:00:00 UTC 2019-05-25 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Course: Introduction to Bioinformatics using NGS data

    20 - 25 May 2019

    Elixir node event
    Course: Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/course-introduction-to-bioinformatics-using-ngs-data-72016a5b-d1c8-4b38-a688-c929f5df2b39 More information will follow 2019-05-20 09:00:00 UTC 2019-05-25 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Course: RaukR

    10 - 21 June 2019

    Elixir node event
    Course: RaukR https://tess.elixir-europe.org/events/course-raukr More information will follow 2019-06-10 09:00:00 UTC 2019-06-21 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • NBIS course: Introduction to Bioinformatics using NGS data

    9 - 14 September 2019

    Elixir node event
    NBIS course: Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/nbis-course-introduction-to-bioinformatics-using-ngs-data More information will follow 2019-09-09 09:00:00 UTC 2019-09-14 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • NBIS course: Data integration, Systems Biology

    9 - 14 September 2019

    Elixir node event
    NBIS course: Data integration, Systems Biology https://tess.elixir-europe.org/events/nbis-course-data-integration-systems-biology More information will follow 2019-09-09 09:00:00 UTC 2019-09-14 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • NBIS course: Bioinformatics for Principal Investigators

    17 - 19 September 2019

    Elixir node event
    NBIS course: Bioinformatics for Principal Investigators https://tess.elixir-europe.org/events/nbis-course-bioinformatics-for-principal-investigators More information will follow 2019-09-17 09:00:00 UTC 2019-09-19 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • NBIS course (prel.): Python programming with applications to bioinformatics

    23 - 28 September 2019

    Elixir node event
    NBIS course (prel.): Python programming with applications to bioinformatics https://tess.elixir-europe.org/events/nbis-course-prel-python-programming-with-applications-to-bioinformatics More information will follow contact: education@nbis.se 2019-09-23 09:00:00 UTC 2019-09-28 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • NBIS course (prel.): ChIP-seq data analysis

    24 - 27 September 2019

    Elixir node event
    NBIS course (prel.): ChIP-seq data analysis https://tess.elixir-europe.org/events/nbis-course-prel-chip-seq-data-analysis More information will follow contact: education@nbis.se 2019-09-24 09:00:00 UTC 2019-09-27 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • NBIS-SIB collaborative course: single-cell transcriptomics

    13 - 19 October 2019

    Elixir node event
    NBIS-SIB collaborative course: single-cell transcriptomics https://tess.elixir-europe.org/events/nbis-sib-collaborative-course-single-cell-transcriptomics More information will follow contact: education@nbis.se 2019-10-13 09:00:00 UTC 2019-10-19 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
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