Extra Resources

workflowr

• Summary
• Checks
• Past versions

Last updated: 2025-05-15

Checks: 2 0

Knit directory: DigitalResearchSkillsNetwork/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: b102ce1

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version b102ce1. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/.RData
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/adit/.DS_Store
    Ignored:    plots/
    Ignored:    raw/

Untracked files:
    Untracked:  analysis/adit/0_content management.csv
    Untracked:  analysis/x202504_Workshop.Rmd

Unstaged changes:
    Deleted:    analysis/202504_Workshop.Rmd
    Modified:   analysis/_site.yml
    Modified:   workflow.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/0_resources.Rmd) and HTML (docs/0_resources.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	b102ce1	DrThomasOneil	2025-05-15	wflow_publish(files)
html	fb553e5	DrThomasOneil	2025-05-14	Build site.
html	cff7923	DrThomasOneil	2025-05-07	Build site.
Rmd	ff95f8f	DrThomasOneil	2025-05-07	wflow_publish(files)
html	16a9613	DrThomasOneil	2025-04-30	Build site.
html	862d6b6	DrThomasOneil	2025-04-29	Build site.
html	938818e	DrThomasOneil	2025-04-14	Build site.
html	ed690e6	DrThomasOneil	2025-04-14	Build site.
html	cb886ef	DrThomasOneil	2025-04-10	Build site.
html	f6c0433	YuchenLi	2025-04-09	Build site.
html	8d78b0f	YuchenLi	2025-04-09	Build site.
html	7421f69	DrThomasOneil	2025-04-08	Build site.
html	f2d3385	DrThomasOneil	2025-03-24	update
html	517dcf9	DrThomasOneil	2025-03-24	Build site.
html	6a4432b	DrThomasOneil	2025-03-24	Build site.
html	1f218f3	DrThomasOneil	2025-03-24	Build site.
html	dca90e9	DrThomasOneil	2025-03-24	Build site.
html	1d1c076	DrThomasOneil	2025-03-24	Build site.
html	956ba9b	DrThomasOneil	2025-03-24	Build site.
Rmd	6b72e34	DrThomasOneil	2025-03-24	wflow_publish(c("analysis/*.Rmd"))
html	d600337	DrThomasOneil	2025-03-18	Build site.
html	b537f69	DrThomasOneil	2025-03-18	Build site.
html	b7982e9	DrThomasOneil	2025-03-16	Build site.
html	fc5dd81	DrThomasOneil	2025-03-16	Build site.
html	8e1c1a3	DrThomasOneil	2025-03-16	Build site.
html	36dc5fc	DrThomasOneil	2025-03-03	Build site.
html	49bb28c	DrThomasOneil	2025-03-03	Build site.
html	8258922	DrThomasOneil	2025-03-03	Build site.
html	71646a5	DrThomasOneil	2025-02-27	Build site.
Rmd	c05aafe	DrThomasOneil	2025-02-27	wflow_publish(c("analysis/*.Rmd"))
html	c7f5738	DrThomasOneil	2025-02-24	Build site.
html	79d09b1	DrThomasOneil	2025-02-24	Build site.
html	a5c9f2c	DrThomasOneil	2025-02-24	Build site.
html	ca2c086	DrThomasOneil	2025-02-24	Build site.
html	fca0503	DrThomasOneil	2025-02-24	Build site.
html	af42fba	DrThomasOneil	2025-02-24	Build site.
html	1aeefc7	DrThomasOneil	2025-02-20	Build site.
html	5fe30de	DrThomasOneil	2025-02-20	Build site.
html	5ef4f12	DrThomasOneil	2025-02-11	Build site.
Rmd	4f9c6de	DrThomasOneil	2025-02-11	update book
html	f48f4f0	DrThomasOneil	2025-02-10	Build site.
html	3bfe847	DrThomasOneil	2025-02-10	Build site.
html	b14f3b5	DrThomasOneil	2025-02-10	Build site.
html	bfba3e0	DrThomasOneil	2025-02-07	Build site.
Rmd	b7989a4	DrThomasOneil	2025-02-07	wflow_publish(c("analysis/*.Rmd"))
html	f3d6f87	DrThomasOneil	2025-02-04	Build site.
html	f654b8d	DrThomasOneil	2025-02-04	Build site.
Rmd	e6ea78d	DrThomasOneil	2025-02-04	wflow_publish(c("analysis/*.Rmd"))
html	4968925	DrThomasOneil	2025-01-30	Build site.
Rmd	afccf59	DrThomasOneil	2025-01-30	wflow_publish(c("analysis/*.Rmd"))
html	299ff3d	DrThomasOneil	2025-01-28	Build site.
Rmd	272b312	DrThomasOneil	2025-01-28	wflow_publish(c("analysis/*"))
html	023005d	DrThomasOneil	2025-01-07	Build site.
html	c893d70	DrThomasOneil	2025-01-06	Build site.
Rmd	8eec2ce	DrThomasOneil	2025-01-06	Initial Deployment
html	660b0f8	DrThomasOneil	2025-01-06	Build site.
html	2e79a1d	DrThomasOneil	2025-01-06	Build site.
Rmd	451a21f	DrThomasOneil	2025-01-06	Initial Deployment

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We’ll drop resources that we find that might be useful to others.

Computational Genomics with R

Computational Genomics with R is an exceptionally comprehensive resource for biomedical bioinformatics. It covers a broad range of topics—statistics, machine learning, sequencing data processing, and more—while providing both code examples and clear explanations. Although it may not be the most accessible starting point for wet-lab researchers, it serves as an invaluable reference for deeper explorations of bioinformatic analyses.

10X Analysis Resources

10X Genomics are a unique company, in that they provide a lot of supporting materials. In the drop down below, we have listed a series of resources that 10X have provided, including how-to videos and tutorials.

Drop-down

Xenium In situ

Downloads and documentation

• Xenium Analysis Overview

• Xenium Onboard Analysis, Xenium Ranger

• Xenium Explorer

Webinars and workshops

• Demystifying single-cell and spatial sequencing data analysis: The path to making biological discoveries routine

• Xenium: Spatial analysis of lung cancers reveals heterogeneity in tumor micro-environments

• Xenium to unravel tumor-immune microenvironment during leptomeningeal metastasis

• Xenium 5k Webinar - Multimodal spatial reconstruction of autoimmune diseases with 5,000-gene assays

Visium HD

Downloads and documentation

• Visium Analysis Overview

• Space Ranger

• Cloud Analysis

  • Cloud Analysis Overview

  • Cloud Analysis Support Documentation

  • Walkthrough Tutorial (with small demo dataset)

• Loupe Browser

  • Tutorials

Webinars and workshops

• Discover spatial insights with intuitive analysis tools for Visium HD data

• Data-driven discovery with Visium Spatial Gene Expression for FFPE

• Spatial transcriptomics data analysis in Python

• Visium HD Bioinformatics bootcamp: Hands-on Visium HD data visualization

Stretchly

Stretchly is an open-source app designed to encourage healthy work habits by prompting regular short (30-second) and long (20-minute) breaks. I’ve found it invaluable for maintaining focus and preventing burnout. It’s highly customizable, allowing you to tailor prompts to your needs.

roadmap.sh

roadmap.sh provides structured learning pathways for various tech-related skills, from Data Science to DevOps. The Data Science and AI roadmap outlines essential topics such as mathematics, statistics, and coding, along with curated free and paid learning resources. These roadmaps are community-driven and frequently updated, making them a great guide for self-paced learning.

LinkedIn Learning

LinkedIn Learning offers a vast library of online courses covering data analysis, programming (including R and Python), statistics, research skills, and professional development. There is a short R for Data Science course that is quite nice.

You should have access to LinkedIn Learning through your University email. Otherwise, WIMR staff can apply for a license through WIMR.

Sydney Informatics Hub

Sydney Informatics Hub offers training workshops regularly on research data management, statistical methods, and high-performance computing. These are more general methods that not only apply to biomedical research, but may provide inspiration or good fundamental knowledge on the analytical methods we use.

Interactive R learning UI

learnr is a package that you can install which provides a nice little UI if you want to practice basicR skills and prefer some interactivity.

ggplot2 book

ggplot2:Elegant Graphics for Data Analysis is a nice, comprehensive handbook for graphing using ggplot2. It covers the basic layout, different graph types, customizing elements such as colours, group overlays, annotations, etc.

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