_pkgdown.yml

reference:
- title: Pre-processing
  desc:  Functions used for pre-processing.
- contents:
  - readData
  - CalMTpercent
  - DetectGeneIDtype
  - QCfun
  - RunSeurat
  - RunGSEA
- title: Visualization of GSEA
  desc:  Functions used for visualization of GSEA Result.
- contents:
  - circleplot
  - clustercorplot
  - Cosine_networkByGSEA
  - edge_bundling_GSEA
  - embeddedplot
  - GOboxplot
  - GOcircleplot
  - gseaHeatmap
  - pathway_unique_shared
  - hierarchyplot_tree
  - pathwayScatterplot
  - ID2Description
  - simplifyEnrichmentplot
  - scPalette
  - scPalette2
  - scPalette3
- title: Topic modeling and visualization
  desc:  Functions used for topic modeling and visualization.
- contents:
  - runLDA
  - cluster_topic_hmp
  - plot_sankey
  - cosineheatmap
  - cosinehmp_cluster
  - cosine_network_cluster
  - cosine_network_term
  - topicProb
  - Topterms_Topic
  - hist_cluster_topic
  - hist_topic_term
  - topicNW1
  - topicNW2
  - topicNW3
  - umap_cluster
  - wordcloud_topic
  - lda.rep
  - plotindex
- title: Transfer topic model
- contents:
  - transfer_LDA
  - cosine_heatmap2
  - cosine_hive
  - cosine_network_cluster2
  - sankey_comparison
- title: Transfer annotation
  desc:  Functions used for annotation transfer from reference to query data.
- contents:
  - oversample_ref
  - predictFun
- title: Built-in Shiny APP
  desc:  Visualize analysis result in Built-in Shiny APP.
- contents:
  - visualize_in_shiny
- title: Data
  desc:  Internal data.
- contents:
  - GO2level
  - HCL_ldaOut
  - MCA_ldaOut
  - MTGENE
  - txid_gene_MT
  - txid_species_gene_MT


articles:
- title: Get started
  navbar: ~
  contents:
  - pre-processing
  - visualization_gsea
  - topicmodel_visualization
  - transfer_topicmodel
  - transfer_annotation
  - shiny_app


---
title: My Document
resource_files:
  - images/shinyappExample.gif
---