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mkdocs.yml
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site_name: MiXCR
site_url: https://mixcr.com/
site_description: "MiXCR: ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling."
site_author: MiLaboratories Inc
copyright: Copyright © MiLaboratories Inc
theme:
name: material
custom_dir: overrides
logo: assets/logo.svg
favicon: assets/favicon.png
palette:
# Palette toggle for light mode
- media: "(prefers-color-scheme: light)"
scheme: default
toggle:
icon: custom/24_moon
name: Switch to dark mode
# Palette toggle for dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
toggle:
icon: custom/24_sun
name: Switch to light mode
# (not all necessary typefaces)
font:
text: IBM Plex Sans
code: IBM Plex Mono
features:
# - navigation.instant # see https://github.com/squidfunk/mkdocs-material/issues/3797
- navigation.tabs
- navigation.top
- navigation.sections
- navigation.tracking
- search.highlight
- search.share
- search.suggest
# - toc.integrate
- content.tabs.link
repo_url: https://github.com/milaboratory/docs
repo_name: milaboratory/docs
edit_uri: edit/main/docs/
plugins:
- search:
lang: en
- minify:
minify_html: true
# - glightbox
- table-reader
markdown_extensions:
- pymdownx.critic
- pymdownx.caret
- pymdownx.keys
- pymdownx.mark
- pymdownx.tilde
- pymdownx.superfences
- pymdownx.tabbed:
alternate_style: true
- pymdownx.inlinehilite
- pymdownx.details
- pymdownx.snippets:
# Fails the build if any imports are missing
check_paths: true
auto_append: [ ]
base_path: [ "docs/mixcr/" ]
- admonition
- attr_list
- def_list
- md_in_html
- markdown_katex:
no_inline_svg: True
insert_fonts_css: True
# macro-file: macros.tex
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.arithmatex:
generic: true
# - toc:
# toc_depth: 3
extra:
generator: false
analytics:
provider: google
property: G-2N4Z95ZG08
extra_css:
- css/extra.css
extra_javascript:
- javascripts/svg.js
- javascripts/onload.js
# - javascripts/mathjax.js
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
nav:
- 'About': mixcr/about.md
- 'Downloads':
- 'Binary distributions': mixcr/getting-started/installation.md
- 'Using with Docker': mixcr/getting-started/docker.md
- 'Obtaining and using license key': mixcr/getting-started/milm.md
- 'First run': mixcr/getting-started/first-run.md
- 'License': mixcr/getting-started/license.md
- 'Support': mixcr/getting-started/support.md
- 'Guides':
- 'Kits & Protocols':
- 'MiLaboratories Human IG RNA Multiplex kit': mixcr/guides/milaboratories-human-bcr-rna-multi.md
- 'MiLaboratories Human TCR RNA Multiplex kit': mixcr/guides/milaboratories-human-tcr-rna-multi.md
- 'MiLaboratories Human TCR DNA Multiplex kit': mixcr/guides/milab-dna-multiplex-tcr.md
- 'SMARTer Human BCR IgG IgM H/K/L Profiling Kit': mixcr/guides/takara-hsa-bcr.md
- 'SMARTer Mouse TCR a/b Profiling Kit': mixcr/guides/takara-mmu-tcr.md
- 'Illumina Ampliseq TCR LR / iRepertoire' : mixcr/guides/iRepertoire.md
- 'QIAseq Immune Repertoire TCR' : mixcr/guides/qiaseq-tcr.md
- 'Cellecta AIR RNA Human': mixcr/guides/cellecta-air-tcr-bcr.md
- 'Cellecta AIR DNA Human': mixcr/guides/cellecta-human-dna-xcr-umi-drivermap-air.md
- 'Cellecta AIR RNA Human Full-length': mixcr/guides/cellecta-human-rna-xcr-full-length-umi-drivermap-air.md
- 'Cellecta AIR RNA Mouse': mixcr/guides/cellecta-mouse-rna-xcr-umi-drivermap-air.md
- 'AbHelix BCR': mixcr/guides/abhelix-bcr.md
- 'BioMed2': mixcr/guides/biomed2-bcr.md
- 'NEBNext Immune Sequencing': mixcr/guides/nebnext-bcr.md
- 'Analysis cases':
- 'Targeted TCR UMI libraries': mixcr/guides/generic-umi-tcr.md
- 'Targeted BCR Multiplex libraries': mixcr/guides/generic-multiplex-bcr.md
- 'Targeted BCR UMI libraries': mixcr/guides/generic-umi-bcr.md
- 'RNA-Seq data' : mixcr/guides/rnaseq.md
- 'Immunoglobulin lineage trees reconstruction': mixcr/guides/ig-trees-reconstruction.md
- 'Special guides':
- 'Comparative Benchmarking of MiXCR and other VDJ analysis tools': mixcr/guides/mixcr-benchmarking.md
- 'Custom reference library': mixcr/guides/create-custom-library.md
- 'Using IMGT library': mixcr/guides/external-libraries.md
- 'B cell lineage tracing': mixcr/guides/b-cell-lineages-webinar.md
- 'Docs':
- 'Overview':
- 'Analysis overview': mixcr/reference/overview-analysis-overview.md
- 'Presets': mixcr/reference/overview-presets.md
- 'Mix-in options list': mixcr/reference/overview-mixins-list.md
- 'Built-in presets': mixcr/reference/overview-built-in-presets.md
- 'Custom reference library': mixcr/guides/create-custom-library.md
- 'Data quality':
- 'MiXCR quality controls': mixcr/reference/qc-overview.md
- 'List of quality checks': mixcr/reference/qc-list-of-checks.md
- 'Sequencing quality issues': mixcr/reference/qc-sequencing-quality.md
- 'Rep-Seq libraries quality issues': mixcr/reference/qc-repseq.md
- 'Non-targeted data quality issues': mixcr/reference/qc-rnaseq.md
- 'MiXCR':
- 'analyze': mixcr/reference/mixcr-analyze.md
- 'align': mixcr/reference/mixcr-align.md
- 'refineTagsAndSort': mixcr/reference/mixcr-refineTagsAndSort.md
- 'assemble': mixcr/reference/mixcr-assemble.md
- 'assemblePartial': mixcr/reference/mixcr-assemblePartial.md
- 'assembleContigs': mixcr/reference/mixcr-assembleContigs.md
- 'findAlleles': mixcr/reference/mixcr-findAlleles.md
- 'findShmTrees': mixcr/reference/mixcr-findShmTrees.md
- 'downsample': mixcr/reference/mixcr-downsample.md
- 'extend': mixcr/reference/mixcr-extend.md
- 'export': mixcr/reference/mixcr-export.md
- 'exportPretty': mixcr/reference/mixcr-exportPretty.md
- 'exportAirr': mixcr/reference/mixcr-exportAirr.md
- 'exportReadsForClones': mixcr/reference/mixcr-exportReadsForClones.md
- 'exportShmTrees': mixcr/reference/mixcr-exportShmTrees.md
- 'exportReports': mixcr/reference/mixcr-exportReports.md
- 'exportReportsTable': mixcr/reference/mixcr-exportReportsTable.md
- 'exportQc': mixcr/reference/mixcr-exportQc.md
- 'exportPlots': mixcr/reference/mixcr-exportPlots.md
- 'exportPreset': mixcr/reference/mixcr-exportPreset.md
- 'exportTables': mixcr/reference/mixcr-exportTables.md
- 'exportPreprocTables': mixcr/reference/mixcr-exportPreprocTables.md
- 'exportClonesOverlap': mixcr/reference/mixcr-exportClonesOverlap.md
- 'groupClones': mixcr/reference/mixcr-groupClones.md
- 'mergeAlignments': mixcr/reference/mixcr-mergeAlignments.md
- 'overlapScatterPlot': mixcr/reference/mixcr-overlapScatterPlot.md
- 'postanalysis': mixcr/reference/mixcr-postanalysis.md
- 'buildLibrary': mixcr/reference/mixcr-buildLibrary.md
- 'mergeLibrary': mixcr/reference/mixcr-mergeLibrary.md
- 'debugLibrary': mixcr/reference/mixcr-debugLibrary.md
- 'qc': mixcr/reference/mixcr-qc.md
- 'Reports':
- 'mixcr align': mixcr/reference/report-align.md
- 'mixcr refineTagsAndSort': mixcr/reference/report-refineTagsAndSort.md
- 'mixcr assemblePartial': mixcr/reference/report-assemblePartial.md
- 'mixcr extend': mixcr/reference/report-extend.md
- 'mixcr assemble': mixcr/reference/report-assemble.md
- 'mixcr assembleContigs': mixcr/reference/report-assembleContigs.md
- 'mixcr findAlleles': mixcr/reference/report-findAlleles.md
- 'mixcr findShmTrees': mixcr/reference/report-findShmTrees.md
- 'RepSeq.io':
- 'fasta': mixcr/reference/repseqio-fasta.md
- 'compile': mixcr/reference/repseqio-compile.md
- 'debug': mixcr/reference/repseqio-debug.md
- 'filter': mixcr/reference/repseqio-filter.md
- 'format': mixcr/reference/repseqio-format.md
- 'fromFasta': mixcr/reference/repseqio-fromFasta.md
- 'fromPaddedFasta': mixcr/reference/repseqio-fromPaddedFasta.md
- 'inferPoints': mixcr/reference/repseqio-inferPoints.md
- 'merge': mixcr/reference/repseqio-merge.md
- 'stat': mixcr/reference/repseqio-stat.md
- 'tsv': mixcr/reference/repseqio-tsv.md
- 'MiTool':
- 'parse': mixcr/reference/mitool-parse.md
- 'filter': mixcr/reference/mitool-filter.md
- 'tag-stat': mixcr/reference/mitool-tag-stat.md
- 'export-fastq': mixcr/reference/mitool-export-fastq.md
- 'correct': mixcr/reference/mitool-refine-tags.md
- 'consensus': mixcr/reference/mitool-consensus.md
- 'process-fastq': mixcr/reference/mitool-process-fastq.md
- 'format-fastq': mixcr/reference/mitool-format-fastq.md
- 'compress-sequence-set': mixcr/reference/mitool-compress-sequence-set.md
- 'Specifications':
- 'Tag pattern': mixcr/reference/ref-tag-pattern.md
- 'Input file name expansion': mixcr/reference/ref-input-file-name-expansion.md
- 'Samples table': mixcr/reference/ref-samples-table.md
- 'Gene features and reference points': mixcr/reference/ref-gene-features.md
- 'Translation rules': mixcr/reference/ref-translation-rules.md
- 'Mutations encoding': mixcr/reference/ref-mutations-encoding.md
# - 'RepSeq.io JSON format': mixcr/reference/ref-repseqio-json-format.md
- 'VDJ.online': https://vdj.online/
- 'Discussions': https://github.com/milaboratory/mixcr/discussions
- 'Github': https://github.com/milaboratory/mixcr