Introduction to research data management, data management planning and services provided by CSC – IT Center for Science
Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project.
Keywords: DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE
Resource type: Series of videos, Video, youtube video
Introduction to research data management, data management planning and services provided by CSC – IT Center for Science
https://www.youtube.com/watch?v=Ol7mniw687E&list=PLD5XtevzF3yEZw-8LadtaGVV8Um6CbMja
http://tess.elixir-uk.org/materials/introduction-to-research-data-management-data-management-planning-and-services-provided-by-csc-it-center-for-science
Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project.
Siiri Fuchs
Minna Ahokas
Maria Lehtivaara
DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE
Researchers
Life Science Researchers
Undergraduate students
Master students
PhD candidates
postdoctoral researchers
Senior Researchers, Lab Managers, Postdocs and PhD Students with basic knowledge of DMPs. Participants in the "Introduction to Data Management Plans" workshop.
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
http://incob2019.org/workshop1/
http://tess.elixir-uk.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
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://www.csc.fi/web/training/-/single-cell-chipster-2019
http://tess.elixir-uk.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.
Eija Korpelainen
Maria Lehtivaara
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://chipster.csc.fi/material/cloud/CloudForTrainers.pdf
http://tess.elixir-uk.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.
Shubham Kapoor
Johan Guldmyr
Jarno Laitinen
Eija Korpelainen
Cloud computing, Containers
Trainers
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://www.csc.fi/en/web/training/-/single-cell-rnaseq-r-2018
http://tess.elixir-uk.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.
Heli Pessa
Bishwa Ghimire
Eija Korpelainen
RNA-Seq
RNA-Seq, Single Cell technologies, scRNA-seq
bioinformaticians
Biologists
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://chipster.csc.fi/manual/courses.html#single-cell
http://tess.elixir-uk.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
Maria Lehtivaara
Eija Korpelainen
RNA-Seq
RNA-Seq, Single Cell technologies, scRNA-seq
Biologists
bioinformaticians
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://chipster.csc.fi/manual/courses.html#16S
http://tess.elixir-uk.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.
Eija Korpelainen
Maria Lehtivaara
Jarno Tuimala
Anu Mikkonen
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://chipster.csc.fi/manual/courses.html#virusdetect
http://tess.elixir-uk.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
Eija Korpelainen
RNA-Seq
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://chipster.csc.fi/manual/courses.html#rna
http://tess.elixir-uk.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
Maria Lehtivaara
Eija Korpelainen
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://www.csc.fi/web/training/-/metagenomics
http://tess.elixir-uk.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
Nils Peder Willassen
Espen Mikal Robertsen
Erik Hjerde
Rob Finn
Anu Mikkonen
Jenni Hultman
Petri Auvinen
Kimmo Mattila
Maria Lehtivaara
Jarno Tuimala
Eija Korpelainen
Metagenomics