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Dataframe manipulation with dplyr

Learning objective:  To be able to use the 6 main dataframe manipulation ‘verbs’ with pipes in dplyr.

Part of a software carpentry online course R for reproducible scientific analysis.

Dataframe manipulation with dplyr

R for reproducible scientific analysis

Software Carpentry

Data:

Gapminder dataset

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Drew LaMar onto Data Manipulation

Data Manipulation in R with dplyr

In this interactive course from DataCamp, you will learn how to to perform sophisticated data manipulation tasks using dplyr. Master the five verbs of data manipulation, and complementing techniques to chain your operations, perform group-wise calculations and access data stored in a database outside R.

Outline:

  • Introduction to dplyr and tbls
  • Select and mutate 
  • Filter and arrange 
  • Summarise and the pipe operator 
  • Group_by and working with databases 

Online course  DataCamp
 

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Drew LaMar onto Data Manipulation

Toxoplasma's Dark Side: The Link Between Parasite and Suicide

...Toxoplasma infection alters rat behavior with surgical precision, making them lose their fear of (and even become sexually aroused by!) the smell of cats by hijacking neurochemical pathways in the rat's brain.

News article

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Drew LaMar onto In the News

Two Studies Strengthen Links Between the Zika Virus and Serious Birth Defects

The Zika virus damages many fetuses carried by infected and symptomatic mothers, regardless of when in pregnancy the infection occurs, according to a small but frightening study released on Friday by Brazilian and American researchers.

News article

Research article  Research article

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Drew LaMar onto In the News

Contingency analysis (cont'd)

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Drew LaMar onto Timeline

Chapter 9: Contingency analysis - associations between categorical variables

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Crows Clever Enough to Learn a Shell Game

This is a great case-study on experimental design and bias.

News  Original paper

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Drew LaMar onto In the News

Fitting probability models to frequency data (cont'd); Contingency analysis

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Drew LaMar onto Timeline

Chapter 8: Fitting probability models to frequency data

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Student and educator materials for a BioInteractive activity on diet and evolution

Students explore the effects of different diets on the evolution of an enzyme that breaks down starch.

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Gabriela Hamerlinck onto Lactase & Amylase

Test1

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Erich Huebner onto p3

Fitting probability models to frequency data (cont'd)

  

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Drew LaMar onto Timeline

Errors in hypothesis testing; Fitting probability models to frequency data

  

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Drew LaMar onto Timeline

Mahler et al. 2013 paper entitled "Exceptional Convergence on the Macroevolutionary Landscape in Island Lizard Radiations"

Abstract: G. G. Simpson, one of the chief architects of evolutionary biology’s modern synthesis, proposed that diversification occurs on a macroevolutionary adaptive landscape, but landscape models are seldom used to study adaptive divergence in large radiations. We show that for Caribbean Anolis lizards, diversification on similar Simpsonian landscapes leads to striking convergence of entire faunas on four islands. Parallel radiations unfolding at large temporal scales shed light on the process of adaptive diversification, indicating that the adaptive landscape may give rise to predictable evolutionary patterns in nature, that adaptive peaks may be stable over macroevolutionary time, and that available geographic area influences the ability of lineages to discover new adaptive peaks.

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Gabriela Hamerlinck onto Anole Evolution

Data from: Exceptional convergence on the macroevolutionary landscape in island lizard radiations

Phylogenetic trees and trait data for Greater Antillean Anolis lizards

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Gabriela Hamerlinck onto Anole Evolution

A phylogenetic activity developed by BioInteractive

This activity supports the film The Origin of Species: Lizards in an Evolutionary Tree. Students are guided to sort the lizard species by appearance, then generate a phylogenetic tree using the lizards’ DNA sequences to evaluate whether species that appear similar are closely related to each other.

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Gabriela Hamerlinck onto Anole Evolution

A film produced by BioInteractive about Anolis lizards

A film produced In the Caribbean islands, adaptation to several common habitats has led to a large adaptive radiation with interesting examples of convergent evolution.

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Gabriela Hamerlinck onto Anole Evolution

Stuart et al. paper in Science "Rapid evolution of a native species following invasion by a congener"

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Gabriela Hamerlinck onto Anole Evolution

All data files from Stuart et al. 2014

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Gabriela Hamerlinck onto Anole Evolution

BioInteractive resources to explore Anole lizard selection

This activity supports the film The Origin of Species: Lizards in an Evolutionary Tree. Students are asked to formulate a hypothesis, and collect and analyze real research data to understand how quickly natural selection can act on specific traits in a population.  

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Gabriela Hamerlinck onto Anole Evolution

Part of the 2013 Holiday Lectures on Science series

In the 2013 Holiday Lectures on Science, leading medical researchers explain how advances in genomics are revolutionizing their work, leading to a better understanding of disease and to improved treatments.

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Gabriela Hamerlinck onto Cancer Genomics

An interacive activity produced by BioInteractive to cencer genomics

Explore the phases, checkpoints, and protein regulators of the cell cycle in this highly interactive Click and Learn and find out how mutated versions of these proteins can lead to the development of cancer.

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Gabriela Hamerlinck onto Cancer Genomics

A set of activities developed by BioInteractive to explore cancer genomics

These two hands-on activities are based on a Howard Hughes Medical Institute 2013 Holiday Lectures on Science video featuring researcher Dr. Charles L. Sawyers.

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Gabriela Hamerlinck onto Cancer Genomics

Vogelstein et al. 2013 paper "Cancer Genome Landscapes"

Abstract: Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of “hills” (genes altered infrequently). To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. A better understanding of these pathways is one of the most pressing needs in basic cancer research. Even now, however, our knowledge of cancer genomes is sufficient to guide the development of more effective approaches for reducing cancer morbidity and mortality.

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Gabriela Hamerlinck onto Cancer Genomics

Coral bleaching animation developed by BioInteractive

Zoom into a coral reef and discover photosynthetic algae inside the coral’s cells. Reef-building corals rely on these symbionts for their survival.

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Gabriela Hamerlinck onto Coral Bleaching