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mkdocs.yml
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site_name: Bioinformatics Documentation
repo_name: melbournebioinformatics/MelBioInf_docs
repo_url: https://github.com/melbournebioinformatics/MelBioInf_docs
# Comment below - old universal analytics tracking. No longer used.
# google_analytics: ['UA-21794901-5', 'www.melbournebioinformatics.org.au/tutorials/']
# needs pip install mkdocs-material
theme:
name: material
custom_dir: overrides
#theme_dir: 'material-theme-overrides' # needs updating for mkdocs 0.17
extra:
feature:
tabs: false
extra_css:
- 'extra.css'
copyright: <a href="https://www.melbournebioinformatics.org.au/">Melbourne Bioinformatics</a>
nav:
- Home: 'index.md'
- 'Tools and skill development':
- 'What is Bioinformatics?': 'guides/bioinfo.md'
- 'Introduction to the Galaxy Platform': 'guides/galaxy.md'
- 'Introduction to Galaxy Workflows': 'tutorials/galaxy-workflows/galaxy-workflows.md'
- 'Introduction to Python': 'tutorials/python_overview/python_overview.md'
- 'Introduction to Git and Github': 'tutorials/using_git/Using_Git.md'
- 'Introduction to Unix': 'tutorials/unix/unix.md'
- 'Introduction to R for Biologists': 'tutorials/intro_R_biologists/intro_R_biologists.md'
- 'Introduction to Genome Browsers': 'tutorials/Genome_browsers/GenomeBrowsers_Intro.md'
- 'RNA-seq Experimental Design': 'tutorials/rna_seq_exp_design/rna_seq_experimental_design.md'
- 'Containerized Bioinformatics': 'tutorials/docker/docker.md'
- 'Common Workflow Language for Bioinformatics': 'tutorials/cwl/cwl.md'
- 'Command-line software development': 'tutorials/bionitio/bionitio.md'
- 'Genomics':
- 'Variant detection':
- 'Introduction to Variant detection': 'tutorials/var_detect_advanced/var_detect_advanced_background.md'
- 'Variant Calling part 1 (Galaxy)': 'tutorials/variant_calling_galaxy_1/variant_calling_galaxy_1.md'
- 'Variant Calling part 2 (Galaxy)': 'tutorials/var_detect_advanced/var_detect_advanced.md'
- 'Long-read Structural Variant Calling': 'tutorials/longread_sv_calling/longread_sv_calling.md'
- 'Variant calling using command-line tools': 'tutorials/variant_calling_gatk1/variant_calling_gatk1.md'
- 'de novo assembly':
- 'Introduction to de novo assembly with Velvet': 'tutorials/assembly/assembly-background.md'
- 'Introduction to de novo genome assembly for Illumina reads': 'tutorials/assembly/assembly-protocol.md'
- 'de novo assembly of Illumina reads using Velvet (Galaxy)': 'tutorials/assembly/assembly.md'
- 'de novo assembly of Illumina reads using Spades (Galaxy)': 'tutorials/assembly/spades.md'
- 'de novo assembly of PacBio reads (unix)': 'tutorials/pacbio/index.md'
- 'Hybrid genome assembly - Nanopore and Illumina': 'tutorials/hybrid_assembly/nanopore_assembly.md'
- 'Metabarcoding':
- 'Introduction to Metabarcoding using Qiime2': 'tutorials/qiime2/qiime2.md'
- 'Transcriptomics':
- 'RNAseq Experimental Design': 'tutorials/rna_seq_exp_design/rna_seq_experimental_design.md'
- 'Bulk RNAseq':
- 'Introduction to bulk RNAseq analysis': 'tutorials/rna_seq_dge_basic/rna_seq_basic_background.md'
- 'RNAseq analysis using HISAT2 (Galaxy)': 'tutorials/rna_seq_dge_basic/rna_seq_basic_tutorial.md'
- 'RNAseq analysis using Tuxedo (Galaxy)': 'tutorials/rna_seq_dge_basic/rna_seq_basic_tuxedo.md'
- 'RNAseq differential expression tool comparision (Galaxy)': 'tutorials/rna_seq_dge_advanced/rna_seq_advanced_tutorial.md'
- 'RNAseq differential expression in R': 'tutorials/rna_seq_dge_in_r/rna_seq_r.md'
- 'Singlecell RNAseq':
- '10X single-cell RNA-seq analysis in R': 'tutorials/singlecell/index.md'
- 'Proteomics':
- 'Identifying proteins from mass spectrometry data': 'tutorials/proteomics_basic/proteomics_basic.md'
- 'Data Formats Background' : 'tutorials/proteomics_basic/background_data_formats.md'
- 'Protein Databases' : 'tutorials/proteomics_basic/background_protein_databases.md'
- 'Search Engines' : 'tutorials/proteomics_basic/background_search_engines.md'
- 'Protein Prophet' : 'tutorials/proteomics_basic/background_protein_prophet.md'
- 'Statistics and Visualisation':
- 'Data visualisation with Python': 'tutorials/python_viz/python_viz.md'
- 'Structural Modelling':
- 'Molecular Dynamics - Introduction to cluster computing': 'tutorials/molecular_dynamics_101/molecular_dynamics_101.md'
- 'Molecular Dynamics - Building input files, visualising the trajectory': 'tutorials/molecular_dynamics_201/molecular_dynamics_201.md'
extra_templates: [
'tutorials/hpc/slides.html',
'tutorials/unix/slides.html',
]
markdown_extensions:
- 'markdown_include.include'
- 'mdx_showable'
- 'markdown.extensions.fenced_code'
- admonition
- smarty
- tables
- codehilite:
linenums: true
- toc:
permalink: true
- pymdownx.arithmatex
- pymdownx.betterem:
smart_enable: all
- pymdownx.caret
- pymdownx.critic
- pymdownx.details
- pymdownx.emoji:
emoji_generator: !!python/name:pymdownx.emoji.to_svg
- pymdownx.inlinehilite
- pymdownx.magiclink
- pymdownx.mark
- pymdownx.smartsymbols
- pymdownx.superfences
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
- markdown.extensions.attr_list