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added the bookdown components; customized the navi bar
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,82 @@ | ||
| 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 | ||
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