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_pkgdown.yml
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_pkgdown.yml
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template:
bootstrap: 5
bslib:
info: "#E6F2FD"
base_font:
google: {family: "Atkinson Hyperlegible", wght: [300, 400, 700], ital: [0, 1]}
headings-color: "#206B72"
link-color: "#216B73"
link-color-dark: "#cef4f9"
link-decoration: underline dotted
reference:
- title: "Read Data"
- contents:
- starts_with("create")
- readLiger
- read10X
- read10XFiles
- as.ligerDataset
- as.liger
- updateLigerObject
- title: "Example Data"
- contents:
- importBMMC
- importCGE
- importPBMC
- pbmc
- pbmcPlot
- bmmc
- deg.marker
- deg.pw
- title: "Preprocessing"
- contents:
- runGeneralQC
- runDoubletFinder
- removeMissing
- normalize
- selectGenes
- scaleNotCenter
- reverseMethData
- downsample
- selectGenesVST
- title: "Integration"
- subtitle: "Perform iNMF and Variants"
- contents:
- runIntegration
- runINMF
- runOnlineINMF
- runUINMF
- runCINMF
- subtitle: "Post-Factorization Alignment"
- contents:
- alignFactors
- quantileNorm
- centroidAlign
- subtitle: "Evaluation"
- contents:
- calcAlignment
- calcAgreement
- calcDatasetSpecificity
- subtitle: "Optimization with New Parameter"
- contents:
- optimizeNewData
- optimizeNewK
- optimizeNewLambda
- optimizeSubset
- title: "Downstream Analysis"
- subtitle: "Dimensionality Reduction"
- contents:
- runUMAP
- runTSNE
- subtitle: "Clustering"
- contents:
- runCluster
- mapCellMeta
- calcARI
- calcPurity
- calcNMI
- subtitle: "Differential Expression"
- contents:
- runMarkerDEG
- runPairwiseDEG
- runWilcoxon
- getFactorMarkers
- subtitle: "GO and GSEA"
- contents:
- runGOEnrich
- runGSEA
- subtitle: "ATAC Specific Analysis"
- contents:
- imputeKNN
- linkGenesAndPeaks
- exportInteractTrack
- title: "Visualization"
- contents:
- starts_with("plot")
- makeRiverplot
- starts_with(".gg")
- starts_with(".plot")
- .complexHeatmapDotPlot
- title: "Object Class"
- contents:
- ends_with("class")
- sub-liger
- sub-sub-liger
- sub-ligerDataset
- rawPeak
- coordinate
- retrieveCellFeature
- subsetLiger
- subsetLigerDataset
- convertOldLiger
- ligerToSeurat
- is.newLiger
- modalOf
- isH5Liger
- restoreH5Liger
- closeAllH5
- title: "Misc"
- contents:
- H5Apply
- commandDiff
- makeFeatureMatrix
- mergeH5
- mergeSparseAll
- writeH5
- title: "Deprecated"
- contents:
- ends_with("deprecated")
- readSubset
- quantileAlignSNF
- getProportionMito
navbar:
title: "rliger"
left:
- text: "Installation"
href: articles/installation.html
- text: "Tutorials"
menu:
- text: "Integrating multiple scRNAseq data"
href: articles/Integrating_multi_scRNA_data.html
- text: "Integrating scRNA and scATAC data"
href: articles/Integrating_scRNA_and_scATAC_data.html
- text: "Online iNMF with HDF5 based data"
href: articles/online_iNMF_tutorial.html
- text: "Integration using unshared features"
href: articles/UINMF_vignette.html
- text: "Cross-species Analysis with UINMF"
href: articles/cross_species_vig.html
- text: "UINMF with STARmap spatial and transcriptomic"
href: articles/STARmap_dropviz_vig.html
- text: "UINMF with SNAREseq scATAC and scRNA"
href: articles/SNAREseq_walkthrough.html
- text: "Integrating scRNAseq and DNA methylation"
href: articles/rna_methylation.html
- text: "Benchmarking integration quality"
href: articles/benchmark.html
- text: "Usage"
menu:
- text: "Import data"
href: articles/import_data.html
- text: "Introduction to a liger object"
href: articles/liger_object.html
- text: "Interoperate with Seurat"
href: articles/liger_with_seurat.html
- text: "Reference"
href: reference/index.html
- text: "NEWS"
href: news/index.html
right:
- text: Welch Lab
href: https://welch-lab.github.io/
- icon: fab fa-github fa-lg
href: https://github.com/welch-lab/liger
- icon: fab fa-twitter fa-lg
href: https://twitter.com/LabWelch