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_pkgdown.yml
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/
_pkgdown.yml
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url: https://alexisvdb.github.io/singleCellHaystack/
template:
# params:
# bootswatch: cerulean
home:
strip_header: true
links:
- text: Learn more
href: https://doi.org/10.1038/s41467-020-17900-3
reference:
- title: Main haystack functions
contents:
- haystack
- haystack_2D
- haystack_highD
- haystack_continuous_highD
- show_result_haystack
- title: Visualization functions
contents:
- plot_gene_haystack
- plot_gene_haystack_raw
- plot_gene_set_haystack
- plot_gene_set_haystack_raw
- plot_rand_fit
- title: Clustering functions
contents:
- hclust_haystack
- hclust_haystack_highD
- hclust_haystack_raw
- kmeans_haystack
- kmeans_haystack_highD
- kmeans_haystack_raw
- title: IO functions
contents:
- read_haystack
- write_haystack
- title: Toy example data
contents:
- dat.expression
- dat.tsne
- title: Background functions
contents:
- default_bandwidth.nrd
- extract_row_dgRMatrix
- extract_row_lgRMatrix
- get_D_KL
- get_D_KL_highD
- get_D_KL_continuous_highD
- get_density
- get_dist_two_sets
- get_euclidean_distance
- get_grid_points
- get_log_p_D_KL
- get_log_p_D_KL_continuous
- get_parameters_haystack
- get_reference
- kde2d_faster
- title: Development
contents:
- plot_compare_ranks
- plot_rand_KLD
navbar:
structure:
left:
- home
- reference
- articles
right: github
components:
home:
icon: fa-home fa-lg
href: index.html
reference:
text: Reference
href: reference/index.html
articles:
text: Articles
menu:
- text: Toy example
href: articles/a01_toy_example.html
- text: Example on scRNA-seq
href: articles/examples/a02_example_scRNAseq.html
- text: Example on Spatial Visium
href: articles/examples/a03_example_spatial_visium.html
- text: Example on Spatial Slide-seqV2
href: articles/examples/a04_example_spatial_slideseqV2.html
- text: Application to MOCA 100k cells
href: articles/examples/a05_moca_100k.html
- text: Application to pseudotime
href: articles/examples/a06_pseudotime.html
- text: Application to gene sets
href: articles/examples/a07_gene_sets.html
#- text: Clustering genes
# href: articles/examples/a08_gene_clustering.html
right:
- icon: fa-github fa-lg
href: https://github.com/alexisvdb/singleCellHaystack