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.

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 6 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
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
Showing 13 upcoming events. Found 43 past events. View all results.
  • Webinar: How to use Techila with Python

    No date given

    Elixir node event
    Webinar: How to use Techila with Python https://tess.elixir-europe.org/events/webinar-how-to-use-techila-with-python This webinar will contain a short introduction to the Techila HPC system and will demonstrate how computational tasks can be pushed to the Techila HPC environment in CSC by using the Python environment on your own computer. https://connect.funet.fi/webinar https://connect.funet.fi/webinar [] [] [] [] [] []
  • Bioweek: Containers, clouds, clusters -combining CSC services in biosciences

    11 - 12 March 2019

    Elixir node event
    Bioweek: Containers, clouds, clusters -combining CSC services in biosciences https://tess.elixir-europe.org/events/bioweek-containers-clouds-clusters-combining-csc-services-in-biosciences CSC provides several alternative platforms for doing bioscience related computing. This course provides overview of these services so that after the course the students know how to choose a right platform combination for their analysis. No previous knowledge is required - the course is suitable for everybody! 2019-03-11 09:00:00 UTC 2019-03-12 17:00:00 UTC CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] [] workshops_and_courses [] []
  • Bioweek: Single cell RNA-seq data analysis using Chipster

    14 - 15 March 2019

    Elixir node event
    Bioweek: Single cell RNA-seq data analysis using Chipster https://tess.elixir-europe.org/events/bioweek-single-cell-rna-seq-data-analysis-using-chipster-ac65eb29-66e9-4d0f-b0ba-2b52dbdd795a This introductory course covers single cell RNA-seq data analysis methods, tools and file formats. The free and user-friendly Chipster software is used in the exercises, and the course is thus suitable for everybody. 2019-03-14 09:00:00 UTC 2019-03-15 16:00:00 UTC CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] [] workshops_and_courses [] []
  • Variant analysis with GATK

    14 - 17 May 2019

    Elixir node event
    Variant analysis with GATK https://tess.elixir-europe.org/events/variant-analysis-with-gatk-2a23a094-4ab3-45de-906e-40d000b7d248 This workshop will focus on the core steps involved in calling variants with the Broad's Genome Analysis Toolkit, using the "Best Practices" developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. 2019-05-14 09:00:00 UTC 2019-05-17 17:00:00 UTC The lecture day 14.5 is organised in Haartman Institute in Lecture hall (luentosali) 2 at Haartmaninkatu 3. The hands-on days 15.-17.5 take place in the computer classroom Dogmi at CSC at Keilaranta 14, Espoo. The best way to reach us is by public transportation; more detailed travel tips are available. The lecture day 14.5 is organised in Haartman Institute in Lecture hall (luentosali) 2 at Haartmaninkatu 3. The hands-on days 15.-17.5 take place in the computer classroom Dogmi at CSC at Keilaranta 14, Espoo. The best way to reach us is by public transportation; more detailed travel tips are available. [] [] [] workshops_and_courses [] []
  • Introduction to Proteomics

    25 March 2019

    Elixir node event
    Introduction to Proteomics https://tess.elixir-europe.org/events/introduction-to-proteomics Proteomics is a systems biology approach to study the entire protein complement of a cell, tissue, or organism. This large-scale study of proteins is increasingly popular in post genomics era and has found its widespread applications in fields including drug discovery, cardiovascular research, and nutrition research, just to name a few. This course will provide both theoretical and practical training at the introductory level. Participants will learn the principles of current methodologies and apply bioinformatics tools for data analysis. 2019-03-25 09:00:00 UTC 2019-03-25 17:00:00 UTC CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] [] workshops_and_courses [] []
  • Bioweek: Understanding your data with R

    13 March 2019

    Elixir node event
    Bioweek: Understanding your data with R https://tess.elixir-europe.org/events/bioweek-understanding-your-data-with-r Beginner course for data carpentry and visualization using R. 2019-03-13 09:00:00 UTC 2019-03-13 17:00:00 UTC CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] [] workshops_and_courses [] []
  • Webinar: Metadata in Science

    20 March 2019

    Elixir node event
    Webinar: Metadata in Science https://tess.elixir-europe.org/events/webinar-metadata-in-science This webinar gives you a quick introductions on metadata usage in research data. Metadata needs to be standardized in order to be able to compare data to other data. Metadata schemes are the overall structure for the metadata. 2019-03-20 14:00:00 UTC 2019-03-20 15:00:00 UTC Join the webinar at Zoom! Link to the room: https://cscfi.zoom.us/j/289605529 Join the webinar at Zoom! Link to the room: https://cscfi.zoom.us/j/289605529 [] [] [] [] [] []
  • Advanced Parallel Programming

    27 February - 1 March 2019

    Elixir node event
    Advanced Parallel Programming https://tess.elixir-europe.org/events/advanced-parallel-programming This course addresses hybrid programming by combining OpenMP and MPI, as well as more advanced topics in MPI. Also, parallel I/O is discussed and exemplified in the course. 2019-02-27 09:00:00 UTC 2019-03-01 16:30:00 UTC CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] [] workshops_and_courses [] []
  • RNA-seq data analysis with Chipster

    6 March 2019

    Elixir node event
    RNA-seq data analysis with Chipster https://tess.elixir-europe.org/events/rna-seq-data-analysis-with-chipster This hands-on course 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 expression analysis. The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required. 2019-03-06 09:00:00 UTC 2019-03-06 17:00:00 UTC The course is organised in the training room Dogmi at CSC, address Keilaranta 14, Espoo, Finland (more information). The course is organised in the training room Dogmi at CSC, address Keilaranta 14, Espoo, Finland (more information). [] [] [] workshops_and_courses [] []
  • CSC Summer School in High-Performance Computing 2019

    25 June - 4 July 2019

    Elixir node event
    CSC Summer School in High-Performance Computing 2019 https://tess.elixir-europe.org/events/csc-summer-school-in-high-performance-computing-2019 CSC Summer School celebrates its 10th anniversary by bringing together undergraduate and graduate students and postdoctoral researchers in different disciplines of scientific computing. The contents consist of lectures and hands-on training on parallel programming, code optimization and other necessary skills in development of scientific software. 2019-06-25 09:00:00 UTC 2019-07-04 17:00:00 UTC Solvalla Sports Institute near the Nuuksio national park in the Helsinki metropolitan area. Solvalla Sports Institute near the Nuuksio national park in the Helsinki metropolitan area. [] [] [] workshops_and_courses [] []
  • Variant analysis workshop

    No date given

    Elixir node event
    Variant analysis workshop https://tess.elixir-europe.org/events/variant-analysis-workshop This course covers several aspects of variant analysis including variant annotation and prioritization. The course consists of three optional days, which participants can combine according to their needs. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] [] [] [] []
  • CSC Summer School in High-Performance Computing 2016

    No date given

    Elixir node event
    CSC Summer School in High-Performance Computing 2016 https://tess.elixir-europe.org/events/csc-summer-school-in-high-performance-computing-2016 The 7th CSC Summer School brings together undergraduate and graduate students and postdoctoral researchers in different disciplines of scientific computing. The contents consist of lectures and hands-on training on parallel programming, code optimization and other necessary skills in development of scientific software. Solvalla sports institute in Nuuksio, a beautiful location in the Helsinki Metropolitan area. Solvalla sports institute in Nuuksio, a beautiful location in the Helsinki Metropolitan area. [] [] [] [] [] []
  • Webinar: How to use Techila with Matlab

    No date given

    Elixir node event
    Webinar: How to use Techila with Matlab https://tess.elixir-europe.org/events/webinar-how-to-use-techila-with-matlab This webinar will contain a short introduction to the Techila HPC system and will demonstrate how computational tasks can be pushed to the Techila HPC environment in CSC by using the MATLAB environment on your own computer. Join the webinar here: https://connect.funet.fi/webinar Join the webinar here: https://connect.funet.fi/webinar [] [] [] [] [] []