Do-It-Yourself Training
Software Carpentry Lessons
Website: Software Carpentry Lessons
Comprehensive lessons for beginners covering:
- The Unix Shell
- Version Control with Git
- Programming with Python
- Plotting and Programming with Python
- Programming with R
- R for Reproducible Scientific Analysis
Additional lessons for domain-specific analyses:
- Genomics: Genomics Lessons
- Ecology: Ecology Lessons
- Geospatial Analysis: Geospatial Lessons
Introduction to Bioinformatics Workbook
Website: Bioinformatics Workbook
Online workbook covering multiple topics related to bioinformatics. Includes videos, detailed explanations and worked examples with links to additional resources. Very extensive covering:
- Command line basics and useful programs (includes Unix basic, introduction to HPC and Bioawk)
- Project Management (Introduction to Slack, GitHub and Markdown)
- Introduction to BLAST
- Experimental Design
- Data acquisition and wrangling (including file transfer, FASTA manipulation; Manipulating Excel data sheets and NCBI SRA)
- Bioinformatics Terminology (Includes section on file formats)
- RNA Sequencing (including section on DGE with DESeq2 and single cell analysis)
- Genome assembly and Annotation (multiple sections and tools)
- Comparative genomics
- Variant Discovery (including FreeBays and GATK Best Practices for DNA-seq)
- Metagenomics
- Genome Repeat Identification
- ATAC-Sequencing
- Data visualisation
Bioconductor – Using R for Bioinformatics
Website: The Bioconductor Help Page
The page has a wealth of workflows and resources across many areas, including a help forum and slack team. Some Software Carpentry Workshops which may also be helpful are:
- Data science with Bioconductor
- Analysis and interpretation of bulk RNA sequencing data with Bioconductor
- Analysis and interpretation of single-cell RNA sequencing data with Bioconductor
- An introduction to the Bioconductor Project
QCIF Training – Statistical Comparisons Using R
Website: Statistical Comparisons Using R
Developed by QCIF and offered as training through CaRST. Prior knowledge of R required. Covers introduction to hypothesis testing; Correlation analysis; Statistical tests for both categorial and continuous variables; ANOVA. Course importantly reviews visualising data, how to choose the right statistical test, and how to interpret results.
Australian BioCommons Training Materials
Website: Australian BioCommons Webinars and Workshops
Lists all past Webinars and Workshops hosted by Australian BioCommons. Within are links to video recordings as well as some of the training materials.
Library Carpentry R Course
Website: Library Carpentry R Course
Designed for beginners to learn R basics, including:
- Data manipulation
- Visualisation
- Statistical analysis
Bioinformatics Hub Resources
- Intro to Bash
- Intro to NGS
- Intro to R for Genomics
- Genomics Applications
- Transcriptomics Applications
RNA-Seq Analysis
- QC & Alignment: QC and Alignment Guide
- Differential Gene Expression Analysis: DESeq2 Tutorial
- Beginner Guide: Beginner’s Guide to DESeq2
- Bulk RNA-seq Gene Expression Analysis
Experimental Design Training
- Basic Experimental Design: Basic Design Guide
- Statistical Experimental Design: Statistical Design Guide
Single-Cell RNA-Seq Training
- Introductory Course: Single-Cell RNA-Seq Course
Spatial Transcriptomics
- Course by S.M. McClatchy: Spatial Transcriptomics Course
Statistical Inference for Biology
Website: Statistical Inference for Biology
A Carpentries Incubator project covering statistical modeling for biological data analysis.
QTL Mapping
In Mice: QTL Mapping in Mice
In Humans:
Snakemake
Website: Snakemake Documentation
Learn to create reproducible workflows for bioinformatics pipelines.
Nextflow
Website: Nextflow Documentation
Guide to implementing scalable, reproducible workflows in high-performance computing environments.
WDL (Workflow Description Language)
Website: WDL Documentation
Learn to develop and execute scalable, reproducible pipelines using WDL. Features include:
- Portable workflow specification language
- Compatibility with Cromwell and miniWDL execution engines
- Tutorials for building workflows in genomics and other domains.
Additional Workshops and Training
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