Workshop General Timings Schedule

Modified

July 1, 2026

Work in progress….

Introduction to R

Episode Duration Approx time
Welcome and opening 25 mins 10–10:25
Environment log in 10 mins 10:25–10:35
Intro to R/Rstudio 40 mins 10:35–11:15
BREAK 10 mins 11:15–11:25
R basics 1.5 hour 11:25–12:30
LUNCH 45 mins 12:30–1:15
R basics 1:15–1:40
Intro to dataset 5 mins 1:40–1:45
R basics contd - factors and df 1 hour 1:45–2:45
BREAK 10 mins 2:45–2:55
Data viz w ggplot2 20 mins 2:55–3:15
Conclusions/Getting help with R ~30 mins 3:15–END
Producing Reports with knitr

Day 1

Episode Duration Approx time
Welcome and opening 25 mins 9:30–9:55
Environment log in 10 mins 9:55–10:05
Intro to R/Rstudio 30 mins 10:05–10:35
BREAK 10 mins 10:35–10:45
R basics 1.5 hrs 10:45–11:40
BREAK 10 mins 11:40–11:50
R basics … 11:50–12:25

Day 2

Episode Duration Approx time
Intro to dataset 5 mins 9:30–9:35
R basics contd - dataframes and manipulation 1 hr 9:35–10:35
BREAK 10 mins 10:35–10:45
Data viz w ggplot2 30 mins 10:45–11:15
BREAK 10 mins 11:15–11:25
Conclusion: Getting help with R 30 mins 11:25–11:55

Visualisation with ggplot2

Single-day workshop, 10am–4pm.

Episode Duration Approx time
Welcome and opening 25 mins 10:00–10:25 am
Environment log in 10 mins 10:25–10:35 am
Visualisation with ggplot2 30 mins 10:35–11:05 am
BREAK 10 mins 11:05–11:15 am
Exploratory analysis 1 hour 11:15–12:15 am
LUNCH 50 mins 12:15–1:05 pm
Exemplar vis 40 mins 1:05–1:45 pm
Building better plots 1.5 hour 1:45–2:20 pm
BREAK 15 mins 2:20–2:35 pm
Building better plots … 2:35–3:30 pm
Close environment END OF DAY

RNA-seq

Two-day workshop.

Day 1

Episode Duration Approx time
Welcome and opening 25 mins 9–9:25
Environment log in 10 mins 9:25–9:35
Background 10 mins 9:35–9:45
Sequence quality 55 mins 9:45–10:10
BREAK 10 mins 10–10:10
Sequence quality 10:10–10:40
Quantifying gene expn 1 hour 10:40–11:10
BREAK 10 mins 11:10–11:20
Quantifying gene expn 11:20–11:50
Exploratory analysis 1 hour 11:50–12:20
BREAK 10 mins 12:20–12:30
Exploratory analysis 12:30–END

Day 2

Episode Duration Approx time
Identify DE genes
t-tests and Pvalues 25 mins 9–9:25
Identify DE w limma 50 mins 9:25–10:00
BREAK 10 mins 10–10:10
Identify DE w limma 10:10–10:25
Identify DE w DEseq2 30 mins 10:25–10:55
BREAK 15 mins 10:55–11:10
Functional analysis 50 mins 11:10–12:00
OPTIONAL BREAK 5–10 mins
General discussion ~30 mins 12:00–END

Reproducibility with Git and Quarto

Two-day workshop.

Day 1 – Git (9:30am–2:30pm)

Episode Duration Approx time
Welcome and opening 25 mins 9:30–9:55 am
Automated version control 5 mins 9:55–10:00 am
Setting up Git 10 mins 10:00–10:10 am
Create a repository 10 mins 10:10–10:20 am
BREAK 10 mins 10:20–10:30 am
Tracking, adding, committing, restoring changes 50 mins 10:30–11:20 am
BREAK 10 mins 11:20–11:30 am
Pushing local changes to github 40 mins 11:30–12:10 pm
LUNCH 50 mins 12:10–1:00 pm
Branches, pulling and merging 40 mins 1:00–1:40 pm
Collaborating and organising your workflow 20 mins 1:40–2:00 pm

Day 2 – Quarto (9:30am–2:30pm)

Episode Duration Approx time
Introduction to Quarto 10 mins 9:30–9:40 am
Getting started 45 mins 9:40–10:25 am
BREAK 10 mins 10:25–10:35 am
Code in qmd files 45 mins 10:35–11:20 am
BREAK 10 mins 11:20–11:30 am
Projects: books and websites 30 mins 11:30–12:00 pm
LUNCH 50 mins 12:00–12:50 pm
Building our own research portfolio 50 mins 12:50–1:40 pm
Optional extra time 1:40–2:30 pm

Introduction to Shell for Bioinformatics

Episode Duration Approx time
Welcome and opening 25 mins 10:00–10:25 am
Environment log in 10 mins 10:25–10:35 am
Overview 5 mins 10:35–10:40 am
First steps - say goodbye to mouse 30 mins 10:40–11:10 am
BREAK 10 mins 11:10–11:20 am
Navigating files and dirs 40 mins 11:20–12:00
Working with files and dirs 55 mins 12:00–12:20
LUNCH 50 mins 12:20–1:10 pm
Working with files and dirs … 1:10–1:45
Redirection 50 mins 1:45–2:20 pm
BREAK 10 mins 2:20–2:30 pm
Redirection … 2:30–2:45 pm
Writing with scripts and working with data 45 mins 2:45–3:30 pm
Project organisation ~5 mins 3:30–3:35 pm

Day 1

Episode Duration Approx time
Welcome and opening 25 mins 09:30–09:55
Environment log in 10 mins 09:55–10:05
Overview 5 mins 10:05–10:10
First steps - say goodbye to mouse 30 mins 10:10–10:40
BREAK 10 mins 10:40–10:50
Navigating files and dirs 40 mins 10:50–11:30
BREAK 10 mins 11:30–11:40
Working with files and dirs 50 mins 11:40–12:30

Day 2

Episode Duration Approx time
Working with files and dirs 10 mins 09:30–09:40
Redirection 50 mins 09:40–10:30
BREAK 10 mins 10:30–10:40
Writing with scripts and working with data 45 mins 10:40–11:25
Project organisation 10 mins 11:25–11:35

Introduction to Bash Scripting and HPC Scheduler

Single-day workshop only, 10am–4pm.

Episode Duration Approx time
Welcome and opening 25 mins 10:00–10:25 am
Environment log in 10 mins 10:25–10:35 am
Background 5 mins 10:35–10:40
Variant calling workflow 1 hour 10:40–11:10
BREAK 10 mins 11:10–11:20
Variant calling workflow … 11:20–11:50
Automating a variant calling workflow 30 mins 11:50–12:20
LUNCH 50 mins 12:20–13:10
RNA-Seq Mapping and Count Data Workflow 1.5 hour 13:10–14:40
BREAK 10 mins 14:40–14:50
Introduction to HPC 10 mins 14:50–15:00
Working with job scheduler 1 hour 15:00–16:00

Intermediate R

Two-day workshop only.

Day 1

Episode Instructor Duration Approx time
Welcome and opening Chloe 25 mins 9–9:25
Environment log in Matt 10 mins 9:25–9:35
Introduction to data Chloe 10 mins 9:20–9:30
String manipulation Chloe 1 hour 9:30–10:30
BREAK 15 mins 10:30–10:45
Relational data Murray 40 mins 10:45–11:25
Functions and conditional statements
part1 Anatomy of functions Murray 40 mins 11:25–11:45
BREAK 15 mins 11:45–12:00
Functions and conditional statements
part1 Anatomy of functions Murray … 12:00–12:20
part2 alpha diversity Matt 40 mins 12:20–1pm

Day 2

Episode Instructor Duration Approx time
part3 improve function design 30 mins 9–9:30
Iterations
part1 for loops 50 mins 9:30–10:40
BREAK 15 mins 10:40–10:55
part2 Pairwise correlation 40 mins 10:55–11:35
part3 rules to iterate by 20 mins 11:35–11:55
BREAK 15 mins 11:55–12:10
Data structures 40 mins 12:10–12:50

Intermediate Shell

Warning

Source spreadsheet flags this schedule as “needs updating — times are incorrect.” Treat the approx times below as unreliable until revised.

Single-day workshop, Day 1 only shown.

Episode Duration Approx time
Welcome and opening 25 mins 10–10:25
Environment log in 5 mins 10:25–10:30
1. Download and verify data 10 mins 10:30–10:40
2. Streams, redirection, pipe 35 mins 10:35–11:10
BREAK 10 mins 11:10–11:20
3. Inspecting + manipulating part1 1hr 10 11:20–12:30
LUNCH 50 mins 12:30–13:20
4. Inspecting + manipulating part2 1 hour 13:20–14:20
BREAK 10 mins 14:20–14:30
4. Inspecting + manipulating part3 45 mins 14:30–15:15
Puzzles 45 mins 15:15–16:00