-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy path_pkgdown.yml
126 lines (108 loc) · 3.07 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
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
url: https://nanostring-biostats.github.io/FastReseg/
template:
bootstrap: 5
bslib:
bg: "#FFF"
fg: "#5A5A5A"
primary: "#A6CE39"
secondary: "#4c9dbb"
success: "#56CC9D"
dark: "#343A40"
code-color: "#6F42C1"
navbar:
bg: "#E6F3FC"
development:
mode: auto
exclude:
- specs.md
- reqs.md
reference:
- title: "Pipeline wrapper"
desc: "Wrapper function to process multi-FOV dataset or per-FOV data"
- contents:
- fastReseg_flag_all_errors
- fastReseg_full_pipeline
- fastReseg_perFOV_full_process
- title: "Preprocessing"
desc: "Functions to prepare input data and get baseline"
- contents:
- runPreprocess
- get_baselineCT
- choose_distance_cutoff
- estimate_MeanProfile
- scoreGenesInRef
- getCellType_maxScore
- getScoreCellType_gene
- title: "Example data"
desc: "Example data to use with tutorial"
- contents:
- has_keyword("datasets")
- title: "Modular functions of pipeline"
desc: "Functions to perform individual tasks for each FOV"
- contents:
- runPreprocess
- runSegErrorEvaluation
- runTranscriptErrorDetection
- runSegRefinement
- title: "Flag poor fitted cells"
desc: "Functions to detect cell segmentation errors"
- contents:
- runSegErrorEvaluation
- score_cell_segmentation_error
- title: "Flag poor fitted transcripts"
desc: "Functions to identify wrongly segmented transcript groups"
- contents:
- runTranscriptErrorDetection
- flag_bad_transcripts
- groupTranscripts_dbscan
- groupTranscripts_Delaunay
- createSpatialDelaunayNW_from_spatLocs
- flagTranscripts_LDA_hyperplane
- title: "Segmentation refinement"
desc: "Functions to evaluate neighborhood of flagged transcript groups and perform refinement"
- contents:
- runSegRefinement
- prepResegDF
- get_neighborhood_content
- getNeighbors_transDF
- decide_ReSegment_Operations
- update_transDF_ResegActions
- transDF_to_perCell_data
- title: "Visualization"
desc: "Auxillary function to visualize spatial pattern of transcript-level information of multiple cells"
- contents:
- plotSpatialScoreMultiCells
- title: "Ultilties"
desc: "Auxillary function to set parallel processing and digesting input files"
- contents:
- numCores
- checkTransFileInputsAndLoadFirst
- prepare_perFOV_transDF
- myFun_fov_load
- title: "Miscellaneous"
desc: "Supporting functions of various purposes"
- contents:
- check_config_leiden
- check_config_spatialNW
- checkAndPrepInputs_perFOV
- checkTypeLengthValue
- compartment_and_add_extra
- initializeAllSegRes
- makeDummyOuts_perFOV
- myFun_3point_singleCell
external-articles:
- name: fastReseg_manuscript
title: Working principles and Manuscript
description: Manuscript for FastReseg describing working principles, performance
characterization and parameter impacts.
href: https://www.biorxiv.org/content/10.1101/2024.12.05.627051v1.abstract
articles:
- title: Manuscript
navbar: ~
contents: fastReseg_manuscript
- title: Tutorial
navbar: Workflow and core functions
contents:
- tutorial
search:
exclude: ['reqs.html', 'specs.html']