Shell | R |SQL | Python | Access

Shell

Topic	Title	Output
Data wrangling	Genomics Shell Intro
Genomics	Genomics Advanced Loops
Genomics	Genomics Advanced Shell
Genomics	Assemble Genomes
Genomics	Genomics Automated Run Variant Calling
Genomics	Download Data
Genomics	Messy Data
Genomics	Organizing Early
Genomics	Genomics Read Quality Trimming
Genomics	Sequence Files Metadata
Genomics	Genomics Shell Data Wrangling
Genomics	Genomics Scripts With Loops
Genomics	Tidy Data Rules
Genomics	Sequence Quality Trimming
Genomics	Variant Calling Workflow 1	[txt]
Genomics	Variant Calling Workflow 2	[txt]
Genomics	Writing Scripts and Working with Data
Genomics	Writing Scripts for Calling Variants
Genomics	Quality Control Software	[txt] [txt] [txt] [txt]
Shell	Files and Directories
Shell	Pipes and Filters
Shell	Sorting
Shell	Working With Wildcards and Files	[txt]
Shell	Shell Beyond Nelle
Shell	Finding Things
Shell	Getting Started
Shell	Shell grep and find
Shell	Shell Scripts With Loops
Shell	Shell Scripts With Loops
Shell	Scripts With Loops Genomics
Shell	Nelles Last Bash

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R

Topic	Title	Output
Basic	Data Management Review	[txt] [txt]
Basic	Vector Review	[txt]
Capstone	Cocili Data Exploration	[png] [png]
Capstone	Length of Floods	[txt]
Combining Basics	Shrub Volume Carbon	[txt]
Data Analysis	Code Shuffle	[jpeg]
Data Frames	Database CSV	[txt]
Data Frames	Shrub Volume Data Frame	[txt]
Debugging	Debug the Code	[txt]
dplyr	Collect from Databases	[txt]
dplyr Databases	Copy to Database	[txt] [txt]
dplyr Databases	Link and Query
dplyr Databases	Manipulate Query	[txt]
dplyr Databases	NEON Mammals	[jpeg] [txt] [jpeg] [jpeg]
dplyr Databases	Source and Query	[txt]
dplyr	Fix the Code	[txt]
dplyr	Link to Databases	[txt] [txt]
dplyr	Shrub Volume Aggregation	[txt]
dplyr	Shrub Volume Data Basics	[txt]
dplyr	Shrub Volume Join	[txt]
Expressions & Variables	Basic Expressions	[txt]
Expressions & Variables	Basic Variables	[txt]
Expressions & Variables	Modify the Code	[txt]
Expressions & Variables	More Variables	[txt]
Expressions & Variables	Variable Reassignment	[txt]
Functions	Built-in Functions	[txt]
Functions	Combining Functions	[txt]
Functions	for Loop	[txt] [txt]
Functions	String Data	[txt]
Functions	Use and Modify	[txt]
Functions	Writing Functions	[txt]
Genomics	Genomics RStudio dplyr	[txt]
Genomics	Genomics RStudio	[txt]
Genomics	Genomics RStudio	[txt]
Genomics	Genomics RStudio	[txt]
Genomics	Genomics RStudio	[txt]
Genomics	Genomics RStudio coercion	[txt] [txt]
Genomics	Genomics RStudio Dataframes
Good Style	Format the Code	[jpeg]
Graphing	Adult vs Newborn Size	[jpeg] [jpeg] [jpeg] [jpeg] [jpeg]
Graphing	Mammal Body Size Distribution	[jpeg] [jpeg] [jpeg] [jpeg] [jpeg]
Graphing	Mass vs Metabolism	[jpeg] [jpeg] [jpeg] [jpeg]
Graphing	Sexual Dimorphism Data Manipulation	[jpeg] [jpeg] [jpeg] [jpeg]
Graphing	Sexual Dimorphism Exploration	[jpeg] [jpeg] [jpeg] [jpeg] [jpeg]
Higher Order Functions	Species Area Relationship	[txt]
Knitr	Reproducible Breeding Bird Survey Analysis	[html]
Loops	Basic Index	[txt]
Loops	Basic Vector	[txt]
Loops	Crown Volume Calculation	[txt] [txt] [png]
Loops	Improve Your Code	[txt]
Loops	Multiple Files	[txt]
Loops	stringr	[txt]
Loops	Use and Modify with Apply	[txt] [txt]
Loops	Use and Modify with Loops	[txt] [txt] [txt]
Making Choices	Choice Operators	[txt]
Making Choices	Choices with Functions	[txt]
Making Choices	Complete the Code	[txt]
Making Choices	DNA or RNA	[txt]
Making Choices	DNA or RNA Iteration	[txt]
Making Choices	Simple If Statement	[txt]
Making Choices	Size Estimates by Name	[txt]
Making Choices	Unit Conversion Challenge	[txt]
Modules	dplyr
NEON	Canopy Height from Space	[png] [png] [png] [png] [txt]
NEON	NEON Database	[jpeg] [jpeg] [jpeg]
NEON	NEON Raster	[jpeg]
NEON	Phenology from Space	[png] [txt]
dplyr	Portal Data Joins	[txt]
dplyr	Portal Data Manipulation	[txt]
Putting It All Together	Size-biased Extinction	[txt] [txt] [png]
Genomics	R-studio
R-SQL	Automate Query	[txt]
R-SQL	Connect and Query	[txt]
R-SQL	Data Stream	[txt]
R-SQL	Export to Database	[txt]
Regular Expressions	Find the Rodents	[txt]
Loops	Climate Space Iteration	[png] [png] [png] [png] [png] [png] [png]
Reproduction	Climate Space Rewrite	[png] [png] [png]
Reproduction	Climate Space	[png] [png] [png] [png] [png] [png] [png] [png] [png] [png] [png] [png] [png]
Reproduction	Dinosaur Size Distribution	[png]
Reproduction	Megafaunal Extinction	[txt] [png] [png] [png]
Scientific	Mammal Body Size	[txt]
Scientific	Mammal Body Size by Continent	[txt]
Scientific	Tree Biomass Challenge	[txt]
Spatial Data	Species Occurrences Elevation Histogram	[png] [png] [png]
Spatial Data	Species Occurrences Map	[png] [png]
SQL Practice	Basic Queries Review	[txt] [txt] [txt]
Statistics	Adult vs Newborn Size Regression	[txt] [jpeg] [jpeg]
Statistics	Mammal Body Size T-test	[txt]
Statistics	Shrub Volume ANOVA	[txt]
Strings	Function with Choices	[txt]
Strings	Long Strings	[txt]
Strings	Print Strings	[txt]
Strings	Split Strings	[txt]
Strings	stringr Functions	[txt]
Strings	Strings and Math	[txt]
Strings	Strings from Data	[txt]
Tests	Test the Code	[txt]
Tidyr	Tree Biomass	[txt]
Vectors	Bird Banding	[txt]
Vectors	Shrub Volume Vectors	[txt]
Version Control	Add and Revert Comment
Version Control Basic	Adding a Remote
Version Control Basic	Commit Multiple Files
Version Control Basic	Create Project Repository
Version Control Basic	First Solo Commit
Version Control Basic	Project Proposal
Version Control Basic	Pulling and Pushing
Version Control Basic	Pushing Changes
Version Control Basic	Second Solo Commit
Version Control Basic	Set Up Git
Version Control	Fix and Commit
Version Control	Git Setup
Version Control	Merge Conflict
Version Control	Pull and Move
Version Control	Revert

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SQL

Topic	Title	Output
Advanced Queries	Aggregated Join	[txt]
Advanced Queries	Basic Join	[txt]
Advanced Queries	Detailed Join	[txt]
Advanced Queries	Filtered Join	[txt]
Advanced Queries	Multi-table Join	[txt]
Advanced Queries	Nesting Queries	[txt]
Aggregation	COUNT	[txt]
Aggregation	SUM	[txt]
Basic Queries	DISTINCT	[txt]
Basic Queries	GROUP BY	[txt]
Basic Queries	ORDER BY	[txt]
Basic Queries	SELECT	[txt] [txt]
Basic Queries	Simple WHERE	[txt] [txt] [txt]
Basic Queries	WHERE	[txt] [txt] [txt]
Database Control	Adding Records	[txt]
Database Control	Creating Tables	[txt]
Database Control	Importing Data	[txt] [txt] [txt]
Database Control	Missing Data	[txt]
Database Control	Updating Records	[txt]
Database Structure	Redundancy	[txt] [txt] [txt]
Database Structure	Split Cells	[txt] [txt]
dplyr Databases	Copy to Database	[txt]
dplyr	Link to Databases	[txt]
QAQC	Data entry validation in Excel
Tidy Data	Improving Messy Data

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Python

Python exercises were used in previous iterations of the course at Utah State University, but are no longer under active development.

Topic	Title	Output
Basic	Data Management Review
Basic	List Review
Combining Basics	Shrub Volume	[txt]
Data Analysis	Code Shuffle
Debugging	Fix the Code 1
Dictionaries	Species Composition 2
Expressions & Variables	Basic Expressions	[txt]
Expressions & Variables	Basic Variables	[txt]
Expressions & Variables	Modify the Code 1	[txt]
Expressions & Variables	More Variables	[txt]
Expressions & Variables	Variable Reassignment
For Loops	Exponential Growth 1
For Loops	Repeat Strings
For Loops	While
Functions	Built-in Functions	[txt]
Functions	for Loop
Functions	GC Content 2	[txt]
Functions	Nested Functions
Functions	Use and Modify	[txt]
Functions	Writing Functions	[txt]
Graphing	Adult vs Newborn Size 1	[png] [png] [png]
Graphing	Mammal Body Size 3	[png]
Graphing	Mass vs Metabolism	[png] [png]
Higher Order Functions	DNA
Higher Order Functions	Species Area Relationship 1
Inheritance	Platypus 4
Libraries	Species Area Relationship 2
List Comprehensions	Platypus 5
Lists	Bird Banding 1	[txt]
Lists	Bird Banding 2
Lists	Bird Banding 3
Lists	DNA Complement 1
Lists	DNA or RNA 2
Lists	Loop
Lists	Nested Lists 1
Lists	Nested Lists 2
Lists	Ultimate Question 2
Loops	Improve Your Code	[txt]
Loops	Shrub Dimensions 1	[txt]
Loops	Shrub Dimensions 2
Loops	Shrub Dimensions 3
Making Choices	Choice Operators	[txt]
Making Choices	DNA or RNA 1	[txt]
Making Choices	GC Content 3
Making Choices	Modify the Code 2	[txt]
Making Choices	Unit Conversion Challenge
Modules	math Functions	[txt]
Object Oriented Programming	Platypus 1
Object Oriented Programming	Platypus 2
Object Oriented Programming	Platypus 3
Problem Decomposition	Exponential Growth 2
Regular Expressions	List the Rodents 1
Regular Expressions	List the Rodents 2
Scientific	DNA Complement 2
Scientific	Mammal Body Size 1	[txt]
Scientific	Mammal Body Size 2	[txt]
Scientific	Shrub Volume 2	[txt]
Scientific	Size-biased Extinction 1
Scientific	Size-biased Extinction 2
Scientific	Tree Biomass
Sets	Species Composition 1
Shell	Bird Counts 1
Shell	Bird Counts 2
Shell	Executable Programs
Shell	Pipes and Filters
Shell	Server
Shell	Finding Things
Shell	Getting Started
Statistics	Adult vs Newborn Size 2	[txt] [png]
Statistics	Mammal Body Size 4	[txt]
Statistics	Shrub Volume 3	[txt]
Strings	GC Content 1	[txt]
Strings	Long Strings	[txt]
Strings	Print Strings	[txt]
Strings	Split Strings	[txt]
Strings	string Functions	[txt]
Strings	string Methods	[txt]
Strings	Strings and Math
Strings	Ultimate Question 1
Tests	Fix the Code 2
Tests	Refactor
Version Control	Add and Revert Comment
Version Control	Fix the Code
Version Control	Merge Conflict
Version Control	Predict Richness
Version Control	Pull and Move
Version Control	Revert
Version Control	Richness Merge Conflict
Version Control	Richness Revert
Version Control	Set Up Git

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Access

Access exercises were used in previous iterations of the course at Utah State University, but are no longer under active development.

Topic	Title	Output
Advanced Queries	Joins 1
Advanced Queries	Joins 2
Advanced Queries	Joins 3
Advanced Queries	Joins 4
Advanced Queries	Nested Queries
Aggregation	Count
Aggregation	Sum
Basic Queries	Filtering
Basic Queries	Grouping 1
Basic Queries	Grouping 2
Basic Queries	Selecting
Basic Queries	Sorting
Database Control	Creating Tables
Database Control	Importing Tables
Database Structure	Redundancy
Database Structure	Split Cells
Database Tools	Forms 1
Database Tools	Forms 2
Database Tools	Forms 3
Database Tools	Reports

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