Contributors: Collins Assisi or Eija Korpelainen
This material is based on CSC's Pouta cloud course which consists of lectures and hands-on exercises 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...
Keywords: Cloud computing, Containers
Resource type: Slides, course materials
This intensive course is to provide students with the prerequisites - some conceptual background and sufficient working knowledge of mathematics - necessary to master the mathematically based graduate courses at the Center for Complex Systems & Brain Sciences. By no means it is intended to...
Scientific topics: Computational biology, Mathematics
Keywords: ComputationalBiology, Neuroscience, complex systems, Mathematics
Resource type: Notes, Scripts
Materials from the asynchronous learning course "ELIXIR eLearning definitions"
Keywords: eLearning, training, EeLP
Resource type: course materials, Training materials, Documentation
Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017
Scientific topics: Transcriptomics, Genomics
Keywords: transcriptomics, RNA-Seq, eLearning, EeLP
Resource type: course materials, Training materials, Slides, Video
This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular 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...
Scientific topics: RNA-Seq
Keywords: RNA-Seq, Single Cell technologies, scRNA-seq
Resource type: course materials
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...
Scientific topics: RNA-Seq
Keywords: RNA-Seq, Single Cell technologies, scRNA-seq
Resource type: course materials, Video
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
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
Metagenomics investigates the composition and function of microbial communities in different environments based on direct isolation of genetic material. It has been accelerated by the advances in high-throughput sequencing technologies, and the increasing data sizes require efficient analysis...
Scientific topics: Metagenomics
Resource type: Video, course materials