/
_pkgdown.yml
107 lines (100 loc) 路 2.66 KB
/
_pkgdown.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
url: https://openbiox.github.io/UCSCXenaShiny/
template:
bootstrap: 5
bootswatch: morph
authors:
Shixiang Wang:
href: https://orcid.org/0000-0001-9855-7357
Shensuo Li:
href: https://github.com/lishensuo
Yi Xiong:
href: https://orcid.org/0000-0002-4370-9824
Longfei Zhao:
href: https://orcid.org/0000-0002-6277-0137
Kai Gu:
href: https://orcid.org/0000-0002-0177-0774
reference:
- title: Data
desc: Builtin datasets and functions to load data
contents:
- load_data
- TCGA.organ
- tcga_clinical
- tcga_surv
- tcga_genome_instability
- tcga_gtex
- tcga_purity
- tcga_subtypes
- tcga_tmb
- tcga_clinical_fine
- ccle_absolute
- ccle_info
- ccle_info_fine
- toil_info
- pcawg_info
- pcawg_purity
- pcawg_info_fine
- title: Data Query
desc: Functions to query data from UCSC Xena data hubs in single molecular level. The functionality of functions below may overlap, we rank them by importance.
contents:
- .opt_pancan
- query_molecule_value
- query_pancan_value
- query_general_value
- query_tcga_group
- query_toil_value_df
- get_pancan_value
- available_hosts
- title: Analysis and Visualiation for Pan-Cancer Study
desc: Functions to analyze and visualize data mainly from TCGA, PCAWG and CCLE
contents:
- tcga_surv_get
- tcga_surv_plot
- analyze_gene_drug_response_asso
- vis_gene_drug_response_asso
- analyze_gene_drug_response_diff
- vis_gene_drug_response_diff
- vis_ccle_tpm
- vis_ccle_gene_cor
- vis_gene_TIL_cor
- vis_gene_immune_cor
- vis_gene_cor
- vis_gene_cor_cancer
- vis_gene_stemness_cor
- vis_gene_tmb_cor
- vis_gene_msi_cor
- vis_gene_pw_cor
- vis_pancan_anatomy
- vis_toil_TvsN
- vis_toil_TvsN_cancer
- vis_toil_Mut
- vis_toil_Mut_cancer
- vis_unicox_tree
- vis_pcawg_dist
- vis_pcawg_gene_cor
- vis_pcawg_unicox_tree
- title: General Analysis and Visualiation
desc: Functions to analyze and visualize general data, i.e., any valid data from UCSC Xena or users
contents:
- vis_identifier_cor
- vis_identifier_multi_cor
- vis_identifier_grp_comparison
- vis_identifier_grp_surv
- vis_dim_dist
- vis_identifier_dim_dist
- ezcor
- ezcor_batch
- ezcor_partial_cor
- title: EDA & Report
desc: Functions for exploratory data analysis and report.
contents:
- mol_quick_analysis
- title: Shiny App
desc: Functions related to Xena Shiny App
contents:
- app_run
- title: Others
desc: Other docs
contents:
- UCSCXenaShiny
- keep_cat_cols