Amanda Devine amdevine

Creating a presentation with Markdown, pandoc, reveal.js, and GitHub Pages

Based on a Vimeo video detailing the process.

Code is written for a Windows PC - may need syntactical changes to work on Mac/Linux.

Substitute your own GitHub username where you see amdevine and your repository name where you see repository-name.

1. Create empty GitHub repository

Access data from the GGBN API

The Global Genome Biodiversity Network (GGBN) API is a service that allows users to retrieve data from the GGBN Data Portal quickly and easily. Data can be accessed via a script or a web browser. Data are output in the JavaScript Object Notation (JSON) format, a common format for sharing and accessing data from websites.

Types of data available

The GGBN API is accessed by using a web browser (or a script) to navigate to a specific URL (the endpoint) on the GGBN website:

http://data.ggbn.org/ggbn_portal/api/search

Information copied from Jill Cates at Medium.

Step 1: Add the remote (original repo that you forked) and call it “upstream”

git remote add upstream https://github.com/original-repo/goes-here.git

Step 2: Fetch all branches of remote upstream

git fetch upstream

Data Carpentry - SQL Cheat Sheet

Query order of operations

SELECT tablea.column1, tablea.column2, tableb.column3 AS somealias, SUM(tableb.column4)
FROM tablea
LEFT JOIN tableb
ON tablea.columnx = tableb.columnx
WHERE (tablea.column1 = 'someString') AND (tablea.column2 = someNumber)

Text was taken from Stackoverflow, user emk. https://stackoverflow.com/a/72156

First, clone a remote Git repository and cd into it:

$ git clone git://example.com/myproject
$ cd myproject

Next, look at the local branches in your repository:

Terrestrial Arthropod Classes

This gist contains all classes that occur in phylum Arthropoda for each data source, and whether these classes would be classified as "terrestrial arthropods" when doing analyses.

Catalogue of Life

Class	Terrestrial Arthropod
Arachnida	Yes
~~Branchiopoda~~	No

Vertebrate Classes

This gist contains all classes that occur in phylum Chordata for each data source, and whether these classes would be classified as vertebrates for the purpose of analysis.

Catalogue of Life

Class	Vertebrate?	Category
Actinopterygii	Yes	Fishes
Amphibia	Yes	Amphibians and Reptiles

	"""
	This script reproduces the functionality of the Real-Time Name Query web app
	found at https://www.globalgeno.me/gaps/live. It is intended to be run as
	a script at the command line. The correct usage is:

	python real_time_name_query.py <names file path> <NCBI API key>
	e.g. python real_time_name_query.py querynames.txt 01234567890ABCDEFGHIK

	Names files should be text files formatted with one name on each line.

	library(tidyverse)

	#### Changing the values in a character/numeric vector ####

	# Create sample data frame
	df <- data.frame(
	col1 = c("A", "A", "A", "A", "B", "B", "B", "B"),
	col2 = c("C", "C", "D", "D", "C", "C", "D", "D"),
	col3 = c("E", "F", "E", "F", "E", "F", "E", "F"),
	stringsAsFactors = FALSE