Peptide cluster to allotype motif correlation report.
+
+
+
+
+
Gibbs Cluster and Reference Motif ComparisonsiEach GibbsCluster motif (left) is paired with its best-matching reference allotype motif (right), ranked by Pearson correlation (PCC). Pick a cluster solution from the dropdown, then use the arrows or dots to step through its clusters. Allele names match the reference logo titles.
+
+ Each cluster solution's GibbsCluster motifs paired with the best-matching
+ reference allotype motif. Use the arrows to step through clusters.
+
+
+
+
+
+
+
+
+
+
+ Results for 1 cluster
+ · 1 motif
+
+
+
+ 1 of 1
+
+
+
+
+
+
+
+
+ 1of1
+ best match HLA-A25:31
+ · PCC 0.745
+ · KLD 7.577
+
+
Top 3 Allotype Matches per ClusteriFor each GibbsCluster motif, the top 3 reference allotypes scoring above the PCC threshold, all interleaved and ranked best first. PCC is the Pearson correlation between the cluster and reference position-weight matrices (1.0 = identical motif). KLD is the GibbsCluster Kullback–Leibler divergence (motif information content). Search by cluster id or allotype.
+
+ Each cluster's 3 best-matching allotypes above the PCC threshold, ranked overall.
+
+
+
+
+
+
+
+
+
#
Cluster
Best HLA/MHC
PCC
KLD
+
+
+
+
+
+
1
+
2of5
+
HLA-B39:124
+
+ 0.893
+
+
1.842
+
+
+
+
2
+
2of5
+
HLA-B3942
+
+ 0.890
+
+
1.842
+
+
+
+
3
+
2of5
+
HLA-B39:82
+
+ 0.889
+
+
1.842
+
+
+
+
4
+
4of6
+
HLA-B39:124
+
+ 0.888
+
+
1.372
+
+
+
+
5
+
4of6
+
HLA-B39:52
+
+ 0.883
+
+
1.372
+
+
+
+
6
+
4of6
+
HLA-B3942
+
+ 0.882
+
+
1.372
+
+
+
+
7
+
2of4
+
HLA-B39:124
+
+ 0.876
+
+
1.960
+
+
+
+
8
+
2of4
+
HLA-B39:47
+
+ 0.872
+
+
1.960
+
+
+
+
9
+
2of4
+
HLA-B39:52
+
+ 0.871
+
+
1.960
+
+
+
+
10
+
1of3
+
HLA-B39:92
+
+ 0.871
+
+
2.366
+
+
+
+
11
+
1of3
+
HLA-B39:66
+
+ 0.867
+
+
2.366
+
+
+
+
12
+
2of3
+
HLA-B5309
+
+ 0.867
+
+
3.771
+
+
+
+
13
+
1of3
+
HLA-B39:69
+
+ 0.863
+
+
2.366
+
+
+
+
14
+
2of3
+
HLA-B53:40
+
+ 0.859
+
+
3.771
+
+
+
+
15
+
2of3
+
HLA-B1513
+
+ 0.852
+
+
3.771
+
+
+
+
16
+
3of4
+
HLA-B44:257
+
+ 0.842
+
+
1.893
+
+
+
+
17
+
3of4
+
HLA-B44:103
+
+ 0.838
+
+
1.893
+
+
+
+
18
+
3of4
+
HLA-B44:188
+
+ 0.838
+
+
1.893
+
+
+
+
19
+
1of6
+
HLA-B44:65
+
+ 0.838
+
+
1.704
+
+
+
+
20
+
1of6
+
HLA-B44:332
+
+ 0.837
+
+
1.704
+
+
+
+
21
+
3of5
+
HLA-B44:332
+
+ 0.837
+
+
1.767
+
+
+
+
22
+
3of5
+
HLA-B44:65
+
+ 0.836
+
+
1.767
+
+
+
+
23
+
1of6
+
HLA-B4429
+
+ 0.835
+
+
1.704
+
+
+
+
24
+
3of5
+
HLA-B44:300
+
+ 0.835
+
+
1.767
+
+
+
+
25
+
1of5
+
HLA-A68:117
+
+ 0.827
+
+
1.764
+
+
+
+
26
+
1of5
+
HLA-A68:45
+
+ 0.827
+
+
1.764
+
+
+
+
27
+
1of5
+
HLA-A6829
+
+ 0.815
+
+
1.764
+
+
+
+
28
+
4of4
+
HLA-B15:418
+
+ 0.806
+
+
2.540
+
+
+
+
29
+
4of4
+
HLA-B1513
+
+ 0.806
+
+
2.540
+
+
+
+
30
+
4of4
+
HLA-B1589
+
+ 0.801
+
+
2.540
+
+
+
+
31
+
5of6
+
HLA-A25:40
+
+ 0.792
+
+
1.944
+
+
+
+
32
+
5of6
+
HLA-A25:41
+
+ 0.792
+
+
1.944
+
+
+
+
33
+
5of6
+
HLA-A25:45
+
+ 0.792
+
+
1.944
+
+
+
+
34
+
6of6
+
HLA-A68:165
+
+ 0.786
+
+
1.469
+
+
+
+
35
+
6of6
+
HLA-A68:85
+
+ 0.784
+
+
1.469
+
+
+
+
36
+
6of6
+
HLA-A68:83
+
+ 0.783
+
+
1.469
+
+
+
+
37
+
2of2
+
HLA-B1589
+
+ 0.777
+
+
4.446
+
+
+
+
38
+
5of5
+
HLA-A25:51
+
+ 0.776
+
+
1.996
+
+
+
+
39
+
5of5
+
HLA-A25:53
+
+ 0.776
+
+
1.996
+
+
+
+
40
+
5of5
+
HLA-A25:57
+
+ 0.776
+
+
1.996
+
+
+
+
41
+
2of2
+
HLA-B5309
+
+ 0.775
+
+
4.446
+
+
+
+
42
+
2of2
+
HLA-B15:418
+
+ 0.773
+
+
4.446
+
+
+
+
43
+
1of2
+
HLA-B3919
+
+ 0.773
+
+
4.108
+
+
+
+
44
+
1of2
+
HLA-B39:121
+
+ 0.768
+
+
4.108
+
+
+
+
45
+
1of2
+
HLA-B39:69
+
+ 0.759
+
+
4.108
+
+
+
+
46
+
1of4
+
HLA-A6807
+
+ 0.747
+
+
2.447
+
+
+
+
47
+
1of1
+
HLA-A25:31
+
+ 0.745
+
+
7.577
+
+
+
+
48
+
1of1
+
HLA-A25:32
+
+ 0.745
+
+
7.577
+
+
+
+
49
+
1of1
+
HLA-A25:34
+
+ 0.745
+
+
7.577
+
+
+
+
50
+
3of6
+
HLA-C12:183
+
+ 0.745
+
+
1.015
+
+
+
+
51
+
3of6
+
HLA-C12:90
+
+ 0.736
+
+
1.015
+
+
+
+
52
+
3of6
+
HLA-C12:213
+
+ 0.731
+
+
1.015
+
+
+
+
53
+
3of3
+
HLA-A6807
+
+ 0.728
+
+
2.738
+
+
+
+
54
+
1of4
+
HLA-A68:105
+
+ 0.726
+
+
2.447
+
+
+
+
55
+
1of4
+
HLA-A6806
+
+ 0.725
+
+
2.447
+
+
+
+
56
+
3of3
+
HLA-A68:88
+
+ 0.715
+
+
2.738
+
+
+
+
57
+
3of3
+
HLA-A6817
+
+ 0.712
+
+
2.738
+
+
+
+
+
+
+
+
+
+
+
Correlation AnalysisiInteractive views of every cluster↔allotype correlation. Drag the PCC threshold to hide weaker matches. The Heatmap colours each pair by PCC; the Network links clusters to their correlated allotypes. The Combined tab stacks both.
+
+
+
+
+ 0.70
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
HeatmapiColour encodes the PCC (0–1) for each cluster × allotype pair above the threshold. Darker = stronger match. Hover a cell for exact values.
+
+
+
+
NetworkiForce-directed graph: each cluster (large coloured node) links to the allotypes it correlates with; edge width scales with PCC. Drag nodes, scroll to zoom, hover for details.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/docs/examples/mouse.html b/docs/examples/mouse.html
new file mode 100644
index 0000000..a4722be
--- /dev/null
+++ b/docs/examples/mouse.html
@@ -0,0 +1,1974 @@
+
+
+
+
+
+
+MHC-TP 2.0.3
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
MHC-TP
+ MHC-TP v2.0.3
+
+
Peptide cluster to allotype motif correlation report.
+
+
+
+
+
Gibbs Cluster and Reference Motif ComparisonsiEach GibbsCluster motif (left) is paired with its best-matching reference allotype motif (right), ranked by Pearson correlation (PCC). Pick a cluster solution from the dropdown, then use the arrows or dots to step through its clusters. Allele names match the reference logo titles.
+
+ Each cluster solution's GibbsCluster motifs paired with the best-matching
+ reference allotype motif. Use the arrows to step through clusters.
+
+
+
+
+
+
+
+
+
+
+ Results for 1 cluster
+ · 1 motif
+
+
+
+ 1 of 1
+
+
+
+
+
+
+
+
+ 1of1
+ best match H-2-Kb
+ · PCC 0.848
+ · KLD 11.813
+
+
Top 3 Allotype Matches per ClusteriFor each GibbsCluster motif, the top 3 reference allotypes scoring above the PCC threshold, all interleaved and ranked best first. PCC is the Pearson correlation between the cluster and reference position-weight matrices (1.0 = identical motif). KLD is the GibbsCluster Kullback–Leibler divergence (motif information content). Search by cluster id or allotype.
+
+ Each cluster's 3 best-matching allotypes above the PCC threshold, ranked overall.
+
+
+
+
+
+
+
+
+
#
Cluster
Best HLA/MHC
PCC
KLD
+
+
+
+
+
+
1
+
1of1
+
H-2-Kb
+
+ 0.848
+
+
11.813
+
+
+
+
2
+
1of2
+
H-2-Db
+
+ 0.807
+
+
3.459
+
+
+
+
3
+
2of2
+
H-2-Kb
+
+ 0.804
+
+
7.510
+
+
+
+
4
+
5of5
+
H-2-Db
+
+ 0.802
+
+
2.152
+
+
+
+
5
+
3of4
+
H-2-Db
+
+ 0.774
+
+
2.214
+
+
+
+
6
+
3of3
+
H-2-Db
+
+ 0.769
+
+
2.415
+
+
+
+
7
+
1of1
+
H-2-Db
+
+ 0.761
+
+
11.813
+
+
+
+
8
+
1of1
+
H-2-Dd
+
+ 0.754
+
+
11.813
+
+
+
+
9
+
4of5
+
H-2-Kb
+
+ 0.746
+
+
4.976
+
+
+
+
10
+
1of5
+
H-2-Kb
+
+ 0.739
+
+
2.161
+
+
+
+
11
+
2of3
+
H-2-Kb
+
+ 0.723
+
+
4.988
+
+
+
+
12
+
1of3
+
H-2-Kb
+
+ 0.716
+
+
3.098
+
+
+
+
13
+
2of4
+
H-2-Kb
+
+ 0.710
+
+
4.204
+
+
+
+
+
+
+
+
+
+
+
Correlation AnalysisiInteractive views of every cluster↔allotype correlation. Drag the PCC threshold to hide weaker matches. The Heatmap colours each pair by PCC; the Network links clusters to their correlated allotypes. The Combined tab stacks both.
+
+
+
+
+ 0.70
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
HeatmapiColour encodes the PCC (0–1) for each cluster × allotype pair above the threshold. Darker = stronger match. Hover a cell for exact values.
+
+
+
+
NetworkiForce-directed graph: each cluster (large coloured node) links to the allotypes it correlates with; edge width scales with PCC. Drag nodes, scroll to zoom, hover for details.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 084ee6e..f8c5514 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -34,7 +34,11 @@ nav:
- Usage: usage.md
- API reference: api.md
- LLM guide: llm.md
- - Example report: example-report.html
+ - Example reports:
+ - Human (class I + II): example-report.html
+ - Human — class I: examples/human-classI.html
+ # - Human — class II: examples/human-classII.html # add when a class II dataset is available
+ - Mouse: examples/mouse.html
plugins:
- search
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+