Learning Materials for Bioscientists

Course materials, eLearning materials, tutorials and webinar recordings for bioscientists.

New: Now also available: RNA-seq pipeline tutorial!

General skills:

• CSC resources for bio users [webinar recording][slides]
• Using HPC environments efficiently [intro to HPC slides] [exercises] [Allas usage materials]
• Migrating bioinformatics analyses from Taito to Puhti [slides] [exercises]
• Data analysis with R [GitHub page]
• Python for Biosciences [course material] [GitHub page][slides][more materials] 
• Using cPouta cloud for bioinformatics [course materials] [slides] [exercises] 
• Python environment in CSC computers [webinar recording]

 

Application focussed:

• Single-cell RNA-seq data analysis [course material] [video lectures] [GitHub page] 
• RNA-seq data analysis  [course material] [pipeline] 
• Protein modeling with Discovery Studio [course material] 
• VirusDetect pipeline [course material] [webinar recording]
• Variant analysis with GATK [course material] [video lectures] [Day 1 materials] [Day 2 materials] [Day 3 materials] [Day 4 materials] 
• Metagenomics data analysis [course material] [video lectures] [pipeline]
• Introduction to proteomics [course material]  [lecture1] [lecture2] [lecture3]  [R demo]  Drug discovery: Schrödinger Maestro [Hands on info] [Hands on files 1] [Hands on files 2] 

 

Chipster:

See the course materials and tutorials for Chipster, our user-friendly graphical user interface for NGS analysis in 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 

 

Archived training material

These guides below are provided for archival purposes. They may contain outdated instructions and references to software and databases that are no longer available at CSC. For up-to-date information please refer to the software list and the web pages of each software package.

• Geenikartoitusopas (PDF, in Finnish)
• Sekvenssianalyysiopas (PDF, in Finnish)