Training materials
Contributors: Alireza Khanteymoori or Anthony Bretaudeau or Armando Arredondo Soto or Charlotte Soneson or Clemens Blank or Marius van den Beek or Mehmet Tekman or Michael Parkin
-
hands-on tutorial
Generating a single cell matrix using Alevin and combining datasets (bash + R)
• beginner10x Single Cell jupyter-notebook paper-replication -
hands-on tutorial
Filter, plot, and explore single cell RNA-seq data with Seurat (R)
• beginner10x R Single Cell jupyter-notebook paper-replication rmarkdown-notebook -
hands-on tutorial
Use Apptainer containers for running Galaxy jobs
• beginnerGalaxy Server administration ansible git-gat jobs -
hands-on tutorial
Hands-on for 'Creating the bulk RNA-seq dataset for deconvolution' tutorial
-
hands-on tutorial
Hands-on for 'Creating the single-cell RNA-seq reference dataset for deconvolution' tutorial
-
hands-on tutorial
Python - Type annotations
•• intermediateSoftware engineering Foundations of Data Science jupyter-notebook -
hands-on tutorial
Long non-coding RNAs (lncRNAs) annotation with FEELnc
•• intermediateGenome Annotation eukaryote -
hands-on tutorial
Hands-on for 'Genome Assembly Quality Control' tutorial
•• intermediateassembly quality control -
slides
Genome assembly quality control.
• beginnerSequence assembly Assembly -
hands-on tutorial
Refining Genome Annotations with Apollo (eukaryotes)
•• intermediateGenome Annotation apollo2 cyoa eukaryote gmod jbrowse1