_pkgdown.yml

title: scMINER
url: https://jyyulab.github.io/scMINER/
template:
  bootstrap: 5
  light-switch: true
  bslib:
    pkgdown-nav-height: 100px
navbar:
  left:
  - text: Quick Tutorial
    href: articles/quick_tutorial.html
  - text: Full Documentation
    href: bookdown/index.html
  - text: Functions
    href: reference/index.html
  right:
  - icon: fa-github
    href: https://github.com/jyyulab/scMINER
reference:
- title: Data preprocessing
  contents: createProjectSpace
- subtitle: Data intake
  desc: Functions to read input data from multiple formats
  contents:
  - readInput_10x.dir
  - readInput_10x.h5
  - readInput_h5ad
  - readInput_table
- subtitle: SparseEset manipulation
  desc: Functions that help create and filter SparseEset objects
  contents:
  - createSparseEset
  - combineSparseEset
  - updateSparseEset
  - filterSparseEset
  - normalizeSparseEset
  - drawSparseEsetQC
- title: MI-based clustering analysis
  desc: Functions that mainly used in clustering analysis
  contents:
  - generateMICAinput
  - addMICAoutput
  - MICAplot
- title: MI-based network inference
  desc: Functions that principally operate for network inference
  contents:
  - getDriverList
  - generateSJARACNeInput
  - drawNetworkQC
  - getActivity_individual
  - getActivity_inBatch
- title: Data visualization and sharing
  desc: Functions that visulize the data analysis and prepare inputs for scMINER Portal
  contents:
  - feature_vlnplot
  - feature_boxplot
  - feature_scatterplot
  - feature_bubbleplot
  - feature_heatmap
  - draw_barplot
  - draw_bubbleplot
  - generatePortalInputs
- title: Differential analysis
  desc: Functions that identify the differntially expressed genes (DEGs) or differentially
    activated drivers (DADs)
  contents:
  - getDE
  - getDA
  - getTopFeatures
- title: Helper functions
  desc: Functions that make the primary functions simpler
  contents:
  - combinePvalVector
  - compare2groups
  - z_normalization
  - get_net2target_list
  - get_target_list2matrix
  - cal_Activity
  - SparseExpressionSet-class
  - pbmc14k_rawCount
  - pbmc14k_expression.eset