Owner

GenomicsAotearoa

10 indexed repositories · View on GitHub

Pangenome-Graphs-Workshop
This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.

HTML · 11 stars
Gene_Regulatory_Networks_Simulation_Workshop

HTML · 7 stars
long-read-assembly
Long-read assembly workshop

CSS · 6 stars
shell-for-bioinformatics
Intermediate-Advanced shell for Bioinformatics

HTML · 5 stars
Intermediate-R
Intermediate R workshop material

HTML · 4 stars
Workshop-Bash_Scripting_And_HPC_Job_Scheduler
A workshop to get you started with automating your genomic data analysis work in a High Performance Computing environment

4 stars
Introduction-to-R
Introduction to R

3 stars
RNA-seq-data-analysis-workflow-NZ
RNAseq workshop using an NZ endemic wrasse species.

SCSS · 1 star
visualization_day
Visualisation is more than just the code used to make a plot.

HTML · 0 stars
data-manipulation-with-tidyverse
WORK IN PROGRESS. Workshop material on genomic data manipulation with tidyverse tools in R

CSS · 0 stars

Beginner friendly Everything

Open All

fix Supp HPC page Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

GenomicsAotearoa/RNA-seq-data-analysis-workflow-NZ#4 · Opened Sep 11, 2026
fix data-files and DataFiles Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

GenomicsAotearoa/RNA-seq-data-analysis-workflow-NZ#3 · Opened Sep 11, 2026
fix code dependancy Open

Difficulty 2/5 1-3 hours Newbie friendliness 64/100

GenomicsAotearoa/RNA-seq-data-analysis-workflow-NZ#2 · Opened Sep 11, 2026
fix section in exploratory analysis Open

GenomicsAotearoa/RNA-seq-data-analysis-workflow-NZ#1 · 1 assignee · Opened Sep 11, 2026
logical subsetting Open

Difficulty 1/5 Under an hour Newbie friendliness 68/100

GenomicsAotearoa/Introduction-to-R#36 · 1 comment · Opened Sep 2, 2026
change flow Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

GenomicsAotearoa/Pangenome-Graphs-Workshop#29 · Opened Aug 28, 2026
typo Open

Difficulty 1/5 Under an hour Newbie friendliness 90/100

GenomicsAotearoa/Pangenome-Graphs-Workshop#28 · 1 comment · Opened Aug 28, 2026
swap text order Open

Difficulty 1/5 Under an hour Newbie friendliness 88/100

GenomicsAotearoa/Pangenome-Graphs-Workshop#27 · Opened Aug 28, 2026
fix images Open

GenomicsAotearoa/Gene_Regulatory_Networks_Simulation_Workshop#4 · 1 assignee · Opened Aug 21, 2026
Update Slurm profiling Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

GenomicsAotearoa/Workshop-Bash_Scripting_And_HPC_Job_Scheduler#7 · Opened Aug 12, 2026
puzzle error Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

GenomicsAotearoa/shell-for-bioinformatics#28 · Opened Aug 7, 2026
material error Open

Difficulty 1/5 Under an hour Newbie friendliness 78/100

GenomicsAotearoa/shell-for-bioinformatics#27 · Opened Aug 7, 2026
puzzle 4 solution Open

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

GenomicsAotearoa/shell-for-bioinformatics#26 · Opened Aug 7, 2026
sed has change @ to a > but @ exists globally. Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

GenomicsAotearoa/shell-for-bioinformatics#25 · Opened Aug 7, 2026
add in a what this workshop does/does not cover section Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

GenomicsAotearoa/shell-for-bioinformatics#23 · Opened Aug 6, 2026
check error lesson 6 variant calling Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

GenomicsAotearoa/Pangenome-Graphs-Workshop#23 · Opened Aug 5, 2026
file name non-existant at odgi step Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

GenomicsAotearoa/Pangenome-Graphs-Workshop#22 · Opened Aug 5, 2026
scale colour explainer Open

GenomicsAotearoa/visualization_day#26 · 1 assignee · Opened Jun 29, 2026
remove polyfill javascript from mkdocs.yml Open

Difficulty 1/5 Under an hour Newbie friendliness 90/100

GenomicsAotearoa/Pangenome-Graphs-Workshop#21 · Opened Jun 7, 2026
add in section from intro R lesson Open

GenomicsAotearoa/data-manipulation-with-tidyverse#1 · 1 assignee · Opened Mar 3, 2026
add stats Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

GenomicsAotearoa/visualization_day#9 · 2 comments · Opened Mar 3, 2026
add in results in alpha diversity section Open

Difficulty 1/5 Under an hour Newbie friendliness 62/100

GenomicsAotearoa/Intermediate-R#11 · Opened Aug 27, 2025
move infix function to appendix/extra Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

GenomicsAotearoa/Intermediate-R#10 · Opened Aug 27, 2025
general issues Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

GenomicsAotearoa/shell-for-bioinformatics#18 · Opened Jul 30, 2025
add a note on how to save intermediate graphs during pggb-odgi runs Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

GenomicsAotearoa/Pangenome-Graphs-Workshop#20 · Opened Jul 26, 2023
5. Evaluating output : .ob input filenames don't match the outputs generated by pggb Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

GenomicsAotearoa/Pangenome-Graphs-Workshop#18 · 1 comment · Opened Jul 25, 2023
Update CutAdapt to Python 3.11 Open

GenomicsAotearoa/long-read-assembly#25 · 1 assignee · Opened Jul 4, 2023
Add notes for instructors - mainly around symlinks, and backups Open

GenomicsAotearoa/long-read-assembly#21 · 1 assignee · Opened Jul 1, 2023
Demo blocks Open

GenomicsAotearoa/Pangenome-Graphs-Workshop#3 · 1 assignee · Opened Jun 13, 2023
Suggested improvements Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

GenomicsAotearoa/shell-for-bioinformatics#14 · 1 comment · Opened Sep 15, 2022

GenomicsAotearoa

Get new issues in your inbox