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mkdocs.yml
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site_name: alakazam
site_url: https://alakazam.readthedocs.io
site_favicon: img/favicon.ico
repo_url: https://github.com/immcantation/alakazam
edit_uri: src/master/docs/
google_analytics: ['G-BDGVJ44VYF', 'https://alakazam.readthedocs.io']
theme:
name: readthedocs
navigation_depth: 2
collapse_navigation: False
sticky_navigation: False
locale: en
titles_only: False
analytics:
gtag: G-BDGVJ44VYF
markdown_extensions:
- admonition
- def_list
- sane_lists
- smarty
- toc:
baselevel: 1
toc_depth: 1-4
permalink: True
docs_dir: docs
nav:
- 'Immcantation Portal': https://immcantation.readthedocs.io/
- 'About':
- 'Introduction': index.md
- 'Download & Installation': install.md
- 'Package Overview': topics/alakazam.md
- 'Release Notes': news.md
- 'Related Projects': projects.md
- 'Vignettes':
- 'How to read and write files': vignettes/Files-Vignette.md
- 'Basic gene usage analysis': vignettes/GeneUsage-Vignette.md
- 'Amino acid physicochemical property analysis': vignettes/AminoAcids-Vignette.md
- 'Analysis of clonal abundance and diversity': vignettes/Diversity-Vignette.md
- 'Using sequencing quality scores': vignettes/Fastq-Vignette.md
- 'Help Topics':
- 'File I/O':
- topics/readChangeoDb.md
- topics/writeChangeoDb.md
- topics/readIgphyml.md
- topics/combineIgphyml.md
- topics/readFastqDb.md
- 'Sequence Cleaning and Manipulation':
- topics/collapseDuplicates.md
- topics/maskSeqEnds.md
- topics/maskSeqGaps.md
- topics/padSeqEnds.md
- topics/translateDNA.md
- topics/isValidAASeq.md
- topics/getPositionQuality.md
- topics/maskPositionsByQuality.md
- topics/junctionAlignment.md
- 'Lineage Reconstruction':
- topics/buildPhylipLineage.md
- topics/graphToPhylo.md
- topics/phyloToGraph.md
- topics/makeChangeoClone.md
- topics/ChangeoClone-class.md
- 'Lineage Topology Analysis':
- topics/getMRCA.md
- topics/getPathLengths.md
- topics/permuteLabels.md
- topics/summarizeSubtrees.md
- topics/tableEdges.md
- topics/testEdges.md
- topics/testMRCA.md
- topics/plotEdgeTest.md
- topics/plotMRCATest.md
- topics/plotSubtrees.md
- topics/EdgeTest-class.md
- topics/MRCATest-class.md
- 'Diversity Analysis':
- topics/calcCoverage.md
- topics/calcDiversity.md
- topics/countClones.md
- topics/estimateAbundance.md
- topics/alphaDiversity.md
- topics/plotAbundanceCurve.md
- topics/plotDiversityCurve.md
- topics/plotDiversityTest.md
- topics/AbundanceCurve-class.md
- topics/DiversityCurve-class.md
- 'Ig and TCR Sequence Annotation':
- topics/countGenes.md
- topics/sortGenes.md
- topics/groupGenes.md
- topics/getSegment.md
- topics/extractVRegion.md
- 'Sequence Distance Calculation':
- topics/getAAMatrix.md
- topics/getDNAMatrix.md
- topics/seqDist.md
- topics/seqEqual.md
- topics/pairwiseDist.md
- topics/pairwiseEqual.md
- topics/nonsquareDist.md
- 'Amino Acid Properties':
- topics/aminoAcidProperties.md
- topics/countPatterns.md
- topics/aliphatic.md
- topics/bulk.md
- topics/charge.md
- topics/gravy.md
- topics/polar.md
- 'Miscellaneous':
- topics/baseTheme.md
- topics/checkColumns.md
- topics/cpuCount.md
- topics/gridPlot.md
- topics/makeTempDir.md
- topics/progressBar.md
- topics/stoufferMeta.md
- topics/translateStrings.md
- 'Data and Constants':
- topics/ExampleDb.md
- topics/ExampleDbChangeo.md
- topics/Example10x.md
- topics/ExampleTrees.md
- topics/SingleDb.md
- topics/ABBREV_AA.md
- topics/IUPAC_CODES.md
- topics/DEFAULT_COLORS.md
- topics/IMGT_REGIONS.md
- 'Deprecated':
- topics/rarefyDiversity.md
- topics/testDiversity.md