Training materials
Difficulty level: Beginner
and Contributors: Alexandre Cormier or Anatole Chessel or CRUK CI Bioinformatics Core or Dr. Alexander Lex or Dr. Colin Combe or Dr. Jim Procter or Dr. Manuel Corpas or Dr. Simon Tomlinson or Jalview Coordinator or Martin Krzywinski or Mehmet Tekman or Vicky Schneider
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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 -
slides
Genome assembly quality control.
• beginnerSequence assembly Assembly -
hands-on tutorial
Masking repeats with RepeatMasker
• beginnerGenome Annotation eukaryote -
hands-on tutorial
Pre-processing of 10X Single-Cell RNA Datasets
• beginnerTranscriptomics 10x Single Cell -
hands-on tutorial
Pre-processing of Single-Cell RNA Data
• beginnerTranscriptomics Single Cell -
hands-on tutorial
Clustering 3K PBMCs with Scanpy
• beginnerTranscriptomics 10x Single Cell -
hands-on tutorial
Analysis of plant scRNA-Seq Data with Scanpy
• beginnerTranscriptomics Single Cell paper-replication plants -
hands-on tutorial
Downstream Single-cell RNA analysis with RaceID
• beginnerTranscriptomics Single Cell -
hands-on tutorial
Bulk RNA Deconvolution with MuSiC
• beginnerTranscriptomics Single Cell transcriptomics
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