srtdisk/_pkgdown.yml at main · mianaz/srtdisk · GitHub

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
url: https://mianaz.github.io/srtdisk/
destination: docs

template:
  bootstrap: 5
  bootswatch: cosmo

development:
  mode: auto

home:
  strip_header: false
  links:
  - text: Browse source code
    href: https://github.com/mianaz/srtdisk

reference:
  - title: "Package Information"
    desc: "Overview and utilities"
    contents:
      - srtdisk-package
      - scdisk
      - IsSCDisk
      - RegisterSCDisk

  - title: "h5Seurat Format"
    desc: "Working with h5Seurat files - the native HDF5-based R/Seurat format"
    contents:
      - SaveH5Seurat
      - LoadH5Seurat
      - h5Seurat-class
      - h5Seurat-bindings
      - Connect
      - h5SI

  - title: "AnnData (h5ad) Format"
    desc: "Converting between Seurat and Python AnnData format"
    contents:
      - H5ADToH5Seurat
      - H5SeuratToH5AD
      - SeuratToH5AD
      - LoadH5AD
      - readH5AD_obs
      - readH5AD_obsm

  - title: "Loom Format"
    desc: "Loading and saving Loom files for interoperability with loompy"
    contents:
      - LoadLoom
      - SaveLoom
      - loom-class
      - loom-bindings
      - LoomLoading
      - ValidateLoom

  - title: "Spatial Data Conversion"
    desc: "Converting spatial data between Seurat and AnnData formats"
    contents:
      - ConvertH5ADSpatialToSeurat
      - ConvertSeuratSpatialToH5AD

  - title: "Format Conversion"
    desc: "General conversion utilities between all supported formats"
    contents:
      - Convert
      - FileType

  - title: "Reading & Writing"
    desc: "Low-level HDF5 reading and writing functions"
    contents:
      - ReadH5
      - as.sparse.H5D
      - WriteH5Group
      - BasicWrite
      - ImageWrite
      - SparseWrite
      - WriteAttribute
      - H5Exists
      - H5Path

  - title: "Object Operations"
    desc: "Utilities for working with HDF5 objects and attributes"
    contents:
      - GetObject
      - AssembleObject
      - AppendData
      - Transpose
      - PadMatrix

  - title: "Testing & Validation"
    desc: "Functions for testing and validating HDF5 files and Seurat objects"
    contents:
      - TestH5
      - TestObject
      - CheckMatrix
      - IsMatrixEmpty

  - title: "Data Type Utilities"
    desc: "Utilities for handling data types and format conversions"
    contents:
      - GuessDType
      - IsDType
      - StringType
      - BoolToInt
      - Dims
      - GetClass
      - GetMargin
      - GetParent
      - SparsePointers
      - ClosestVersion
      - ChunkPoints
      - MakeSpace

  - title: "Metadata & Attributes"
    desc: "Working with HDF5 attributes and metadata"
    contents:
      - PadNames
      - RandomName
      - Timestamp
      - UpdateKey
      - UpdateSlots
      - FixFeatures
      - CompoundToGroup
      - Writeable
      - WriteMode