Tutorials & Code
Links to various tutorials and code used by our lab:
Bioinformatics (mostly written for Linux Ubuntu):
Local BLAST: Protocol for finding target species in an eDNA data set generated using Nanopore Sequencing.
Simple Bash Shell Scripts and Related Programs:
Combining files with Cat. Using Cat to combine files.
AWK sequence size filter. Bash command to filter a fasta file by size using the awk command.
Computing and printing FASTA file DNA fragment sizes. Bash script to compute and print DNA fragment sizes in a FASTA file from eDNA studies.
Counting the number of sequences in several files. Bash script to count the number of sequences in many files and list the result by file.
Using Grep to find and manipulate strings. Basics on using grep from the command line.
Converting fastq files to fasta files with SED. This one-liner converts fastq files generated from genomic applications to traditional fasta files.
Separating sequences by barcode. Bash script to separate DNA sequences by a single barcode and place them in individual folders/files.
Excel script to reverse complement DNA sequences. Visual Basic for Applications (VBA) Function in Excel to Reverse Complement DNA Sequences.
Renaming Files in a Folder from the Bash Command Line. Removing the first Eight Characters of Every File Name.
Command Line (general):
Aguirre Lab Linux Cheat Sheet. A Linux command cheat sheet for our lab.
Linux Cheat Sheet- Cheat sheet for Linux shell commands.
LinuxCommand.org- Link to The Linux Command Line book by William Shotts.
The Unix Shell- Shell tutorial with exercises.
Python Tutorials & Code:
The Python Tutorial- From Python.org.
Conda Tutorials & Code:
Conda - Getting started. A basic guide to getting started with Conda, an environment control system for bioinformatics. Runs from the terminal in Linux.
R Tutorials: General
Beginning Work in R Tutorial. Short tutorial to begin work in R.
R Tutorials: Managing and Summarizing Data
Computing Group Descriptive Statistics with dplyr. Short tutorial for using dplyr to calculate descriptive statistics by group.
Converting R data frames to Excel Spreadsheets. Short tutorial for using openxlsx to convert R data frames to Excel spreadsheets.
R Tutorials: Graphing
ggplot2 Quick Reference: color (and fill) from SAPE.
Scatter Plot Tutorial. Tutorial for making simple scatter plots in RStudio and ggplot2.
Scatter Plot for Publications Tutorial. Second tutorial for making publication quality scatter plots in RStudio and ggplot2.
Scatter Plot with Vertical and Horizontal Error Bars Tutorial. Tutorial for making simple scatter plots with error bars in RStudio and ggplot2.
Scatter Plots with Regression Lines and Confidence Intervals Tutorial. Tutorial for making scatter plots with Regression Lines and Confidence Intervals in RStudio and ggplot2.
Line Graphs For Multiple Groups Tutorial. Tutorial for making publication quality line graphs with multiple groups in RStudio and ggplot2.
Box Plot Tutorial. Tutorial for making simple box plots in RStudio and ggplot2.
Pie Chart Tutorial. Tutorial for making simple pie charts in RStudio using default graphics.
Grouped Bar Graph Tutorial. Tutorial for making a grouped bar graph in RStudio and ggplot2.
R Tutorials: Basic Statistics
R Basic Statistics: t-test Tutorial. Tutorial for conducting, one-sample, two-sample and paired-sample t-tests in R Studio.
R Basic Statistics: ANOVA. Tutorial for conducting the analysis of variance (ANOVA) in R Studio.
R Basic Statistics: Correlation. Tutorial for conducting a correlation analysis in R Studio.
R Basic Statistics: Regression. Tutorial for conducting linear regression in R Studio.
R Basic Statistics: ANCOVA. Tutorial for conducting the analysis of covariance (ANCOVA) in R Studio.
Fisher's Exact Test. Tutorial for running Fisher's Exact Test in R Studio
R Tutorials: Multivariate Analysis
Linear Mixed Models in R: Tutorial by Olivia Schweikart
Linear Modeling. Tutorial for conducting Linear Modeling in R Studio.
PCA. Tutorial for conducting Principal Component Analysis (PCA) in R Studio.
R Tutorials: External Tutorials and Guides
The R Project for Statistical Computing
R Studio- Interface for using R.
R Tutorial- An Online R Tutorial.
Learning R- PDF of book by Ricard Cotton.
Modern Statistics with R. Online book by Mans Thulin.
Modern Statistics for Modern Biology. Online book on Statistics in R and Bioconductor by Susan Holmes and Wolfgang Huber.
R for Data Science- Online version of book by Wickham & Grolemund.
Computational Genomics with R - Online book by Altuna Akalin.
R Graphics Cookbook- Online version of book by Winston Chang.
R Markdown- R Markdown: The Definitive Guide by Yihui Xie, J. J. Allaire, Garrett Grolemund.
Beyond Multiple Linear Regression. Applied Generalized Linear Models and Multilevel Models in R. Online book by Paul Roback and Julie Legler.
Geometric Morphometrics:
Geometric Morphometrics undergraduate lab. An undergraduate lab activity introducing geometric morphometrics that I use in my Evolution course. Github link with lab protocol, data files, and specimen images. Runs in MorphoJ.
Code for running a basic PCA on geometric morphometric data in Geomorph (R). Code for conducting a basic PCA in Geomorph (R).
Setting Sliding Semilandmarks in Geomorph. Tutorial for setting sliding landmarks for defining outlines in the R package Geomorph.
3D Slicer: Program for working with micro-CT scan data
Getting Started With 3D Slicer. Tutorial for opening a fish micro-CT scan image file in 3D Slicer and visualizing the skeleton.
Segmenting an Individual Skeleton From a Bulk Scan. Tutorial for separating individuals from a bulk scan of several individuals.
Cleaning Up the Segmented Skeleton. Tutorial for how to clean up a segmented skeleton, removing bone fragments of other fish and debris from the image.
QGIS:
QGIS. Link to open source QGIS program for creating geographic maps.
Youtube tutorial for adding latitude and longitude points to a map in QGIS.
Youtube tutorial: QGIS Basemaps - The ultimate tutorial.
Useful External Tutorials and Code (Github/Other):
Adaptation Genomics Workshop Materials. By Claire Merot - Github page.
Bionformatics Cheat Sheet (Illumina). By Christoph Hahn - Github page.
Discriminant Analysis of Principal Components (DAPC). By Grünwald et al.
A Short Introduction to Docker for Bioinformatics. By Christoph Hahn - Github page.
Introduction to Genome-Wide Association Studies (GWAS). By Filippo Biscarini, Oscar Gonzalez-Recio, Christian Werner.
Metabarpark. R scripts for reformatting metabarcoding databases by Owen S. Wangensteen - Github page.
UiT Metabarcoding. DUFA, MJOLNIR, CommunR- Github page.
Phylogenomics Tutorial Based on BUSCO Genes. By Christoph Hahn - Github page.
denovo assembly RAD analysis. By Mark Ravinet - Github page.
Last updated: August 26, 2024
Bioinformatics (mostly written for Linux Ubuntu):
Local BLAST: Protocol for finding target species in an eDNA data set generated using Nanopore Sequencing.
Simple Bash Shell Scripts and Related Programs:
Combining files with Cat. Using Cat to combine files.
AWK sequence size filter. Bash command to filter a fasta file by size using the awk command.
Computing and printing FASTA file DNA fragment sizes. Bash script to compute and print DNA fragment sizes in a FASTA file from eDNA studies.
Counting the number of sequences in several files. Bash script to count the number of sequences in many files and list the result by file.
Using Grep to find and manipulate strings. Basics on using grep from the command line.
Converting fastq files to fasta files with SED. This one-liner converts fastq files generated from genomic applications to traditional fasta files.
Separating sequences by barcode. Bash script to separate DNA sequences by a single barcode and place them in individual folders/files.
Excel script to reverse complement DNA sequences. Visual Basic for Applications (VBA) Function in Excel to Reverse Complement DNA Sequences.
Renaming Files in a Folder from the Bash Command Line. Removing the first Eight Characters of Every File Name.
Command Line (general):
Aguirre Lab Linux Cheat Sheet. A Linux command cheat sheet for our lab.
Linux Cheat Sheet- Cheat sheet for Linux shell commands.
LinuxCommand.org- Link to The Linux Command Line book by William Shotts.
The Unix Shell- Shell tutorial with exercises.
Python Tutorials & Code:
The Python Tutorial- From Python.org.
Conda Tutorials & Code:
Conda - Getting started. A basic guide to getting started with Conda, an environment control system for bioinformatics. Runs from the terminal in Linux.
R Tutorials: General
Beginning Work in R Tutorial. Short tutorial to begin work in R.
R Tutorials: Managing and Summarizing Data
Computing Group Descriptive Statistics with dplyr. Short tutorial for using dplyr to calculate descriptive statistics by group.
Converting R data frames to Excel Spreadsheets. Short tutorial for using openxlsx to convert R data frames to Excel spreadsheets.
R Tutorials: Graphing
ggplot2 Quick Reference: color (and fill) from SAPE.
Scatter Plot Tutorial. Tutorial for making simple scatter plots in RStudio and ggplot2.
Scatter Plot for Publications Tutorial. Second tutorial for making publication quality scatter plots in RStudio and ggplot2.
Scatter Plot with Vertical and Horizontal Error Bars Tutorial. Tutorial for making simple scatter plots with error bars in RStudio and ggplot2.
Scatter Plots with Regression Lines and Confidence Intervals Tutorial. Tutorial for making scatter plots with Regression Lines and Confidence Intervals in RStudio and ggplot2.
Line Graphs For Multiple Groups Tutorial. Tutorial for making publication quality line graphs with multiple groups in RStudio and ggplot2.
Box Plot Tutorial. Tutorial for making simple box plots in RStudio and ggplot2.
Pie Chart Tutorial. Tutorial for making simple pie charts in RStudio using default graphics.
Grouped Bar Graph Tutorial. Tutorial for making a grouped bar graph in RStudio and ggplot2.
R Tutorials: Basic Statistics
R Basic Statistics: t-test Tutorial. Tutorial for conducting, one-sample, two-sample and paired-sample t-tests in R Studio.
R Basic Statistics: ANOVA. Tutorial for conducting the analysis of variance (ANOVA) in R Studio.
R Basic Statistics: Correlation. Tutorial for conducting a correlation analysis in R Studio.
R Basic Statistics: Regression. Tutorial for conducting linear regression in R Studio.
R Basic Statistics: ANCOVA. Tutorial for conducting the analysis of covariance (ANCOVA) in R Studio.
Fisher's Exact Test. Tutorial for running Fisher's Exact Test in R Studio
R Tutorials: Multivariate Analysis
Linear Mixed Models in R: Tutorial by Olivia Schweikart
Linear Modeling. Tutorial for conducting Linear Modeling in R Studio.
PCA. Tutorial for conducting Principal Component Analysis (PCA) in R Studio.
R Tutorials: External Tutorials and Guides
The R Project for Statistical Computing
R Studio- Interface for using R.
R Tutorial- An Online R Tutorial.
Learning R- PDF of book by Ricard Cotton.
Modern Statistics with R. Online book by Mans Thulin.
Modern Statistics for Modern Biology. Online book on Statistics in R and Bioconductor by Susan Holmes and Wolfgang Huber.
R for Data Science- Online version of book by Wickham & Grolemund.
Computational Genomics with R - Online book by Altuna Akalin.
R Graphics Cookbook- Online version of book by Winston Chang.
R Markdown- R Markdown: The Definitive Guide by Yihui Xie, J. J. Allaire, Garrett Grolemund.
Beyond Multiple Linear Regression. Applied Generalized Linear Models and Multilevel Models in R. Online book by Paul Roback and Julie Legler.
Geometric Morphometrics:
Geometric Morphometrics undergraduate lab. An undergraduate lab activity introducing geometric morphometrics that I use in my Evolution course. Github link with lab protocol, data files, and specimen images. Runs in MorphoJ.
Code for running a basic PCA on geometric morphometric data in Geomorph (R). Code for conducting a basic PCA in Geomorph (R).
Setting Sliding Semilandmarks in Geomorph. Tutorial for setting sliding landmarks for defining outlines in the R package Geomorph.
3D Slicer: Program for working with micro-CT scan data
Getting Started With 3D Slicer. Tutorial for opening a fish micro-CT scan image file in 3D Slicer and visualizing the skeleton.
Segmenting an Individual Skeleton From a Bulk Scan. Tutorial for separating individuals from a bulk scan of several individuals.
Cleaning Up the Segmented Skeleton. Tutorial for how to clean up a segmented skeleton, removing bone fragments of other fish and debris from the image.
QGIS:
QGIS. Link to open source QGIS program for creating geographic maps.
Youtube tutorial for adding latitude and longitude points to a map in QGIS.
Youtube tutorial: QGIS Basemaps - The ultimate tutorial.
Useful External Tutorials and Code (Github/Other):
Adaptation Genomics Workshop Materials. By Claire Merot - Github page.
Bionformatics Cheat Sheet (Illumina). By Christoph Hahn - Github page.
Discriminant Analysis of Principal Components (DAPC). By Grünwald et al.
A Short Introduction to Docker for Bioinformatics. By Christoph Hahn - Github page.
Introduction to Genome-Wide Association Studies (GWAS). By Filippo Biscarini, Oscar Gonzalez-Recio, Christian Werner.
Metabarpark. R scripts for reformatting metabarcoding databases by Owen S. Wangensteen - Github page.
UiT Metabarcoding. DUFA, MJOLNIR, CommunR- Github page.
Phylogenomics Tutorial Based on BUSCO Genes. By Christoph Hahn - Github page.
denovo assembly RAD analysis. By Mark Ravinet - Github page.
Last updated: August 26, 2024