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  • CSC - IT Center for Science

    CSC - IT Center for Science Ltd. is a non-profit, state-owned company administered by the Finnish...

    9 training materials
    0 upcoming events (61 past events)
    CSC - IT Center for Science https://tess.elixir-europe.org/content_providers/csc-it-center-for-science CSC - IT Center for Science Ltd. is a non-profit, state-owned company administered by the Finnish Ministry of Education and Culture. CSC maintains and develops the state-owned centralised IT infrastructure and uses it to provide nationwide IT services for research, libraries, archives, museums and culture as well as information, education and research management. CSC has the task of promoting the operational framework of Finnish research, education, culture and administration. As a non-profit, government organisation, it is our duty to foster exemplary transparency, honesty and responsibility. Trust is the foundation of CSC's success. Customers, suppliers, owners and personnel alike must feel certain that we will fulfil our commitments and promises in an ethically sustainable manner. CSC has offices in Espoo's Keilaniemi and in the Renforsin Ranta business park in Kajaani. /system/content_providers/images/000/000/016/original/c65ddc42-63fc-44da-8d0f-9f88c54779d7?1469458451
    • Showing 9 materials.
    Single cell RNA-seq data analysis with R

    This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and...

    Scientific topics: RNA-Seq

    Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

    Resource type: course materials

    Single cell RNA-seq data analysis with R https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-with-r This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime analysis. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq bioinformaticians Biologists
    Single cell RNA-seq data analysis using Chipster

    This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3...

    Keywords: scRNA-seq

    Resource type: Slides, Training materials

    Single cell RNA-seq data analysis using Chipster https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-using-chipster This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3 tools embedded in the user-friendly Chipster software. scRNA-seq Biologists bioinformaticians
    Detecting differentially expressed genes with RNA-seq 11.9.2019

    This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and...

    Scientific topics: RNA-Seq

    Detecting differentially expressed genes with RNA-seq 11.9.2019 https://tess.elixir-europe.org/materials/detecting-differentially-expressed-genes-with-rna-seq This workshop introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential gene expression analysis. The workshop consists of lectures and practical exercises. The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required, and the workshop is thus suitable for everybody. RNA-Seq
    Metagenomics data analysis

    This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of...

    Scientific topics: Metagenomics

    Resource type: Video, course materials

    Metagenomics data analysis https://tess.elixir-europe.org/materials/metagenomics-data-analysis This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of amplicon sequencing data (16S rRNA). Finally, international databases and standards for storing the data are introduced. The course material includes slides, exercises and lecture videos. The workshop is organized in collaboration with the ELIXIR EXCELERATE project and PRACE, and it is part of the PRACE Advanced Training Centre activity. Eija Korpelainen Metagenomics
    RNA-seq data analysis

    This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises,...

    Scientific topics: RNA-Seq

    Resource type: course materials, Video

    RNA-seq data analysis https://tess.elixir-europe.org/materials/rna-seq-data-analysis-with-chipster This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
    Virus detection using small RNA-seq

    This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....

    Scientific topics: RNA-Seq

    Resource type: course materials, Video

    Virus detection using small RNA-seq https://tess.elixir-europe.org/materials/virus-detection-using-small-rna-seq This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
    Community analysis of amplicon sequencing data (16S rRNA)

    This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the...

    Resource type: course materials, Video

    Community analysis of amplicon sequencing data (16S rRNA) https://tess.elixir-europe.org/materials/community-analysis-of-amplicon-sequencing-data-16s-rrna This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
    Single cell RNA-seq data analysis with Chipster

    This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also...

    Scientific topics: RNA-Seq

    Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

    Resource type: course materials, Video

    Single cell RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430 This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq Biologists bioinformaticians
    Introduction to using cloud and containers for training - OpenStack and Docker oriented view

    This material is based on CSC's [Pouta cloud course](https://www.csc.fi/en/web/training/-/pouta-cloud-course-2018) which consists of lectures and hands-on [exercises](https://chipster.csc.fi/material/cloud/exercises.pdf) on creating and managing virtual resources in OpenStack (VM, volumes,...

    Keywords: Cloud computing, Containers

    Resource type: Slides, course materials

    Introduction to using cloud and containers for training - OpenStack and Docker oriented view https://tess.elixir-europe.org/materials/introduction-to-using-cloud-and-containers-for-training-openstack-and-docker-oriented-view This material is based on CSC's [Pouta cloud course](https://www.csc.fi/en/web/training/-/pouta-cloud-course-2018) which consists of lectures and hands-on [exercises](https://chipster.csc.fi/material/cloud/exercises.pdf) on creating and managing virtual resources in OpenStack (VM, volumes, networks, security Groups, VM snapshots, etc). It also covers topics like orchestration with Heat and accessing Pouta Object storage. The original material was produced by Shubham Kapoor and Johan Guldmyr, and it was tailored for trainers by Jarno Laitinen. Eija Korpelainen Cloud computing, Containers Trainers
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