Beginner course
Bioinformatics
You already work at the bench. This course takes you from the data explosion to a first sequence alignment, without setting up a computer first.
Start chapter 1
Five short scenes. No install.
A worldview for bioinformatics
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Computing basics and a first loop
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Regular expressions for sequence
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A first script: let a loop do the repeats
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Treat an error like a lab result
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Quality control, the gel of sequencing
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From raw reads to a QC report
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The logic under sequence analysis
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Why alignment is the foundation
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Pairwise alignment: the match that costs least
Locked - 14
Why BLAST can search a database so fast
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Multiple alignment and the conserved core
Locked - 16
Trees and a gene's history
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Finding genes in a genome
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Real variants versus sequencing error
Locked - 19
Assembly: a book from a million scraps
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From genes to a tree
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A shared pattern for omics
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What a transcriptome measures
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Sample tables and annotation tables
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Why raw counts are not expression
Locked - 24
Alignment or pseudoalignment
Locked - 25
Is a difference in expression real
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Volcano plots and heatmaps
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Enrichment: a gene list into a story
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Batch effects
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Single cells, not only the average
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From raw data to a biological claim
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From analysis to careful science
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Statistics that prevent most analysis mistakes
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Versions, notes, and reruns
Locked - 33
Figures that carry the biology
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From a result to a careful claim
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Public data, no new experiment
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What bioinformatics can and cannot answer
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