Relaxation Techniques for the Upset Data Scientist ·...
Transcript of Relaxation Techniques for the Upset Data Scientist ·...
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Relaxation Techniques for the Upset Data Scientist
Nils Gehlenborg, PhD
http://gehlenborglab.org | @nils_gehlenborg
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What are the sources of your tension and anger?
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Xu et al., Nature Communications 3, 1258 (2014)
Where is the biggest intersection?
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Rat Genome Sequencing Consortium, Nature 428, 493 (2004)
“Rats,” you’ll say, “I’ll go bananas!”
D’Hont et al., Nature 488, 213 (2012)
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Why is this stressful and exhausting?
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This visualization makes you work!
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This visualization makes you work!
[Good] visualization uses
perception to free up cognition!
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What does that mean?
453 x 862 = ?
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What does that mean?
453 x 862 =906
+ 27,180+ 362,400
390,486
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What are some proven relaxation techniques?
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EGFR 76
PTEN87
TP5380
4422
5
19
43
941
Lex & Gehlenborg, Nature Methods 11, 1 (2014)
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
1. Let Go!
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
2. Stretch!
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
3. Align!
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
4. Gather!
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
5. Sort!
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
6. Let Go! (again)
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
Inte
rsec
tion
Size
Set Size
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
44 4341
2219
9
5
80
76
87
Inte
rsec
tion
Size
Set Size
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
44 4341
2219
9
5
80
76
87
Inte
rsec
tion
Size
Set Size
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
TP53
EGFR
PTEN
44 4341
2219
9
5
80
76
87
Inte
rsec
tion
Size
Set Size
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Lex & Gehlenborg, Nature Methods 11, 1 (2014)
TP53
EGFR
PTEN
44 4341
2219
9
5
80
76
87
Inte
rsec
tion
Size
Set Size
EGFR 76
PTEN87
TP5380
4422
5
19
43
941
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Conway, Lex, Gehlenborg, Bioinformatics 2017
Hey! It’s an UpSet Plot!
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Disclaimer
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A ⋂ B A ⋃ B B \ A
http://en.wikipedia.org/wiki/Venn_diagram
Venn Diagrams are actually very useful!
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I am hiring postdocs!
HARVARD MEDICAL SCHOOL DEPARTMENT OF BIOMEDICAL INFORMATICS
See http://gehlenborglab.org or http://dbmi.med.harvard.edu for details.
Data visualization, analysis, and management for: • genomic structural variants • dynamics of the 3D genome • cancer subtypes in patient cohorts • exploration tools for data repositories • provenance graphs