ProtPipe2/_pkgdown.yml at main · NIH-CARD/ProtPipe2 · 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
url: https://nih-card.github.io/ProtPipe2/docs/
template:
  bootstrap: 5

reference:
  - title: "Input"
    contents:
      - protpipe_example_se
      - create_se
      - create_se_from_olink
      - create_se_from_soma
      - detect_intensity_cols
      - convert_numeric_cols
      - olink_all_output
      - soma_all_output
      - run_protpipe_shiny

  - title: "Quality Control"
    contents:
      - get_pg_counts
      - plot_pg_counts
      - plot_pg_intensities
      - get_CVs
      - plot_CVs
      - get_sample_correlation
      - plot_correlation_heatmap

  - title: "Pre-Processing"
    contents:
      - lod_filter
      - apply_min_intenisty
      - filter_unique_proteins
      - filter_overlap
      - filter_proteins_by_percent
      - filter_outlier_samples
      - log2_transform
      - z_score
      - mean_normalize
      - median_normalize
      - impute
      - impute_min
      - impute_left_dist
      - batch_correct
      - generate_preprocessing_report
      - has_step

  - title: "Clustering / Dimensionality Reduction"
    contents:
      - get_PCs
      - plot_PCs
      - plot_hierarchical_cluster
      - get_umap
      - plot_umap

  - title: "Differential Expression"
    contents:
      - filter_features
      - do_limma_binary
      - do_t_test_binary
      - do_comparison_continuous
      - plot_volcano
      - plot_correlation_volcano
      - add_entrez
      - read_ontology
      - enrich_go
      - enrich_kegg
      - enrich_terms
      - gse_go
      - gse_kegg
      - gse_terms
      - enrich_pathways

  - title: "Abundance Profiling"
    contents:
      - compare_protein
      - plot_proteomics_heatmap