Learning Materials for Bioscientists

Here you can find verious course materials, e-learning materials, tutorials, and webinar recordings for bioscientists.

For upcoming courses, see our training calendar. For e-learning materials, check our course offering on e-Lena platform. On CSC Docs platform, we have a learning material bank and lots of tutorials on various subjects, including bioinformatics.

You may find useful trainings and materials also on ELIXIR's TeSS portal.

General

• CSC resources for bio users [webinar recording-CSC resources for bio users] [slides-CSC resources for bio users]
• Using CSC computing environments efficiently [-CSC Computing environmente-learning page] [slides] [tutorials & exercises-Using CSC HPC environments efficiently] [Running your first job on Puhti tutorial]
• Elements of supercomputing [-Elements of Supercomputinge-learning page]
• Biocontainers [course materials-Biocontainers] [-Biocontainerse-learning page] [Singularity tutorial]
• Data analysis with R [GitHub page-Data analysis with R]
• Python for biosciences [course material-Python for Biosciences] [GitHub page-Python for Biosciences]
• Using cPouta cloud for bioinformatics [course materials-cPouta cloud for bioinformatics] [slides-cPouta cloud for bioinformatics] [exercises-cPouta cloud for bioinformatics] 
• Python environment on CSC computers [webinar recording-Python environment in CSC computers]
• See also the self-study materials for introduction to Python and R on our More Python and R study materials onNotebooks platform

Application-focused

• Single-cell RNA-seq data analysis [course material-Single-cell RNA-seq data analysis] [video lectures-Single-cell RNA-seq data analysis] [GitHub page-Single-cell RNA-seq data analysis]  [e-learning course-Single-cell RNA-seq data analysis]
• RNA-seq data analysis  [course material-RNA-seq data analysis ] [RNA-seq analysispipeline] 
• Protein modeling with Discovery Studio [course material-Protein modeling with Discovery Studio] 
• VirusDetect pipeline [course material-VirusDetect pipeline] [webinar recording-VirusDetect pipeline]
• Variant analysis with GATK [course material-Variant analysis with GATK] [video lectures-Variant analysis with GATK]
• Metagenomics data analysis [course material-Metagenomics data analysis] [video lectures-Metagenomics data analysis]
• Drug discovery: Schrödinger Maestro [hands-on infoabout Schrödinger Maestro] [hands-on files 1-Schrödinger Maestro] [hands-on files 2-Schrödinger Maestro] 

Chipster

See the course materials and tutorials for Chipster, our user-friendly graphical user interface for NGS analysis on Chipster course materials page. Topics covered include:

• RNA-seq data analysis
• Single cell RNA-seq data analysis
• Virus detection using small RNA-seq
• Community analysis of amplicon sequencing data (16S)
• Detection and annotation of genomic variants
• ChIP-seq data analysis
• Microarray data analysis