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circos

data viewer with comparative genomics in mind

martin krzywinski

Click on an image to view next image. Download presentation as pdf png jpg pptx ppt. More about Circos. Circos - data viewer - introduction - page 1 Circos - data viewer - introduction - page 2 Circos - data viewer - introduction - page 3 Circos - data viewer - introduction - page 4 Circos - data viewer - introduction - page 5 Circos - data viewer - introduction - page 6 Circos - data viewer - introduction - page 7 Circos - data viewer - introduction - page 8 Circos - data viewer - introduction - page 9 Circos - data viewer - introduction - page 10 Circos - data viewer - introduction - page 11 Circos - data viewer - introduction - page 12 Circos - data viewer - introduction - page 13 Circos - data viewer - introduction - page 14 Circos - data viewer - introduction - page 15 Circos - data viewer - introduction - page 16 Circos - data viewer - introduction - page 17 Circos - data viewer - introduction - page 18 Circos - data viewer - introduction - page 19 Circos - data viewer - introduction - page 20 Circos - data viewer - introduction - page 21 Circos - data viewer - introduction - page 22 Circos - data viewer - introduction - page 23 Circos - data viewer - introduction - page 24 Circos - data viewer - introduction - page 25 Circos - data viewer - introduction - page 26 Circos - data viewer - introduction - page 27 Circos - data viewer - introduction - page 28 Circos - data viewer - introduction - page 29 Circos - data viewer - introduction - page 30 Circos - data viewer - introduction - page 31 Circos - data viewer - introduction - page 32 Circos - data viewer - introduction - page 33 Circos - data viewer - introduction - page 34 Circos - data viewer - introduction - page 35 Circos - data viewer - introduction - page 36 Circos - data viewer - introduction - page 37 Circos - data viewer - introduction - page 38 Circos - data viewer - introduction - page 39 Circos - data viewer - introduction - page 40 Circos - data viewer - introduction - page 41 Circos - data viewer - introduction - page 42 Circos - data viewer - introduction - page 43 Circos - data viewer - introduction - page 44 Circos - data viewer - introduction - page 45 Circos - data viewer - introduction - page 46 Circos - data viewer - introduction - page 47 Circos - data viewer - introduction - page 48 Circos - data viewer - introduction - page 49 Circos - data viewer - introduction - page 50 Circos - data viewer - introduction - page 51 Circos - data viewer - introduction - page 52 Circos - data viewer - introduction - page 53 Circos - data viewer - introduction - page 54

news + thoughts

Beyond Belief Campaign BRCA Art

Wed 11-06-2025

Fuelled by philanthropy, findings into the workings of BRCA1 and BRCA2 genes have led to groundbreaking research and lifesaving innovations to care for families facing cancer.

This set of 100 one-of-a-kind prints explore the structure of these genes. Each artwork is unique — if you put them all together, you get the full sequence of the BRCA1 and BRCA2 proteins.

Propensity score weighting

Mon 17-03-2025

The needs of the many outweigh the needs of the few. —Mr. Spock (Star Trek II)

This month, we explore a related and powerful technique to address bias: propensity score weighting (PSW), which applies weights to each subject instead of matching (or discarding) them.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Propensity score weighting. (read)

Kurz, C.F., Krzywinski, M. & Altman, N. (2025) Points of significance: Propensity score weighting. Nat. Methods 22:1–3.

Happy 2025 π Day—
TTCAGT: a sequence of digits

Thu 13-03-2025

Celebrate π Day (March 14th) and sequence digits like its 1999. Let's call some peaks.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2025 π DAY | TTCAGT: a sequence of digits. The digits of π are encoded into DNA sequence and visualized with Sanger sequencing. (details)

Crafting 10 Years of Statistics Explanations: Points of Significance

Sun 09-03-2025

I don’t have good luck in the match points. —Rafael Nadal, Spanish tennis player

Points of Significance is an ongoing series of short articles about statistics in Nature Methods that started in 2013. Its aim is to provide clear explanations of essential concepts in statistics for a nonspecialist audience. The articles favor heuristic explanations and make extensive use of simulated examples and graphical explanations, while maintaining mathematical rigor.

Topics range from basic, but often misunderstood, such as uncertainty and P-values, to relatively advanced, but often neglected, such as the error-in-variables problem and the curse of dimensionality. More recent articles have focused on timely topics such as modeling of epidemics, machine learning, and neural networks.

In this article, we discuss the evolution of topics and details behind some of the story arcs, our approach to crafting statistical explanations and narratives, and our use of figures and numerical simulations as props for building understanding.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Crafting 10 Years of Statistics Explanations: Points of Significance. (read)

Altman, N. & Krzywinski, M. (2025) Crafting 10 Years of Statistics Explanations: Points of Significance. Annual Review of Statistics and Its Application 12:69–87.

Propensity score matching

Mon 16-09-2024

I don’t have good luck in the match points. —Rafael Nadal, Spanish tennis player

In many experimental designs, we need to keep in mind the possibility of confounding variables, which may give rise to bias in the estimate of the treatment effect.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Propensity score matching. (read)

If the control and experimental groups aren't matched (or, roughly, similar enough), this bias can arise.

Sometimes this can be dealt with by randomizing, which on average can balance this effect out. When randomization is not possible, propensity score matching is an excellent strategy to match control and experimental groups.

Kurz, C.F., Krzywinski, M. & Altman, N. (2024) Points of significance: Propensity score matching. Nat. Methods 21:1770–1772.

Understanding p-values and significance

Tue 24-09-2024

P-values combined with estimates of effect size are used to assess the importance of experimental results. However, their interpretation can be invalidated by selection bias when testing multiple hypotheses, fitting multiple models or even informally selecting results that seem interesting after observing the data.

We offer an introduction to principled uses of p-values (targeted at the non-specialist) and identify questionable practices to be avoided.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Understanding p-values and significance. (read)

Altman, N. & Krzywinski, M. (2024) Understanding p-values and significance. Laboratory Animals 58:443–446.

Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentrePHSA
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