Training materials
Target audience: Students
and Authors: Bérénice Batut or The Carpentries
and Contributors: Ajay Pillai or Célia Michotey or Erasmus+ Programme or Helena Rasche or John Davis
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hands-on tutorial
Data visualisation Olympics - Visualization in R
• beginnerSoftware engineering Foundations of Data Science R cyoa jupyter-notebook rmarkdown-notebook -
hands-on tutorial
Identification of AMR genes in an assembled bacterial genome
• beginnerWhole genome sequencing Public health and epidemiology Genomics Microbiology Sequence analysis Infectious disease Antimicrobial Resistance Genome Annotation amr gmod illumina jbrowse1 microgalaxy one-health -
hands-on tutorial
Python - Coding Style
•• intermediateSoftware engineering Foundations of Data Science jupyter-notebook -
hands-on tutorial
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
• beginnerSequence assembly Whole genome sequencing Public health and epidemiology Genomics Microbiology Antimicrobial Resistance Assembly amr assembly gmod jbrowse1 microgalaxy nanopore -
hands-on tutorial
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
• beginnerSequence assembly Whole genome sequencing Public health and epidemiology Genomics Microbiology Assembly assembly illumina microgalaxy -
hands-on tutorial
Reference-based RNA-Seq data analysis
• beginnerTranscriptomics QC bulk collections cyoa drosophila rna-seq -
hands-on tutorial
RNA Seq Counts to Viz in R
• beginnerTranscriptomics interactive-tools -
hands-on tutorial
Variant Calling Workflow
• beginnerSoftware engineering Foundations of Data Science -
hands-on tutorial
SQL with R
•• intermediateSoftware engineering Foundations of Data Science R SQL jupyter-notebook rmarkdown-notebook -
hands-on tutorial
SQL with Python
•• intermediateSoftware engineering Foundations of Data Science Python SQL jupyter-notebook