Rebuilding sundries.

inst/rebook/references.csv

@@ -1,9 +1,9 @@
 id,file,text
-advanced-options,advanced-options.html,6
-preconstructed-indices,advanced-options.html,6.1
-parallelization,advanced-options.html,6.2
-approximate-algorithms,advanced-options.html,6.3
-cluster-level-annotation,advanced-options.html,6.4
+advanced-options,advanced-options.html,7
+preconstructed-indices,advanced-options.html,7.1
+parallelization,advanced-options.html,7.2
+approximate-algorithms,advanced-options.html,7.3
+cluster-level-annotation,advanced-options.html,7.4
 annotation-diagnostics,annotation-diagnostics.html,4
 overview-2,annotation-diagnostics.html,4.1
 based-on-the-scores-within-cells,annotation-diagnostics.html,4.2
@@ -17,39 +17,43 @@ fig:grun-beta-heat,annotation-diagnostics.html,4.4
 fig:grun-beta-heat2,annotation-diagnostics.html,4.5
 fig:grun-beta-heat-all,annotation-diagnostics.html,4.6
 fig:grun-label-clusters,annotation-diagnostics.html,4.7
-bibliography,bibliography.html,10
+bibliography,bibliography.html,11
 classic-mode,classic-mode.html,2
 overview,classic-mode.html,2.1
 annotating-the-test-dataset,classic-mode.html,2.2
 interaction-with-quality-control,classic-mode.html,2.3
 choices-of-assay-data,classic-mode.html,2.4
 reference-choice,classic-mode.html,2.5
-contributors,contributors.html,9
-cross-annotating-mouse-brains,cross-annotating-mouse-brains.html,8
-loading-the-data-1,cross-annotating-mouse-brains.html,8.1
-applying-the-annotation-1,cross-annotating-mouse-brains.html,8.2
-diagnostics-1,cross-annotating-mouse-brains.html,8.3
-comparison-to-clusters-1,cross-annotating-mouse-brains.html,8.4
-fig:unref-brain-score-heatmap,cross-annotating-mouse-brains.html,8.1
-fig:unref-brain-delta-dist,cross-annotating-mouse-brains.html,8.2
-fig:unref-brain-marker-heat,cross-annotating-mouse-brains.html,8.3
-fig:unref-brain-label-clusters,cross-annotating-mouse-brains.html,8.4
-fig:unref-brain-label-tsne,cross-annotating-mouse-brains.html,8.5
+contributors,contributors.html,10
+cross-annotating-mouse-brains,cross-annotating-mouse-brains.html,9
+loading-the-data-1,cross-annotating-mouse-brains.html,9.1
+applying-the-annotation-1,cross-annotating-mouse-brains.html,9.2
+diagnostics-1,cross-annotating-mouse-brains.html,9.3
+comparison-to-clusters-1,cross-annotating-mouse-brains.html,9.4
+fig:unref-brain-score-heatmap,cross-annotating-mouse-brains.html,9.1
+fig:unref-brain-delta-dist,cross-annotating-mouse-brains.html,9.2
+fig:unref-brain-marker-heat,cross-annotating-mouse-brains.html,9.3
+fig:unref-brain-label-clusters,cross-annotating-mouse-brains.html,9.4
+fig:unref-brain-label-tsne,cross-annotating-mouse-brains.html,9.5
+exploiting-the-cell-ontology,exploiting-the-cell-ontology.html,6
+motivation-1,exploiting-the-cell-ontology.html,6.1
+basic-manipulation,exploiting-the-cell-ontology.html,6.2
+adjusting-resolution,exploiting-the-cell-ontology.html,6.3
 introduction,introduction.html,1
 motivation,introduction.html,1.1
 method-description,introduction.html,1.2
 quick-start,introduction.html,1.3
 where-to-get-help,introduction.html,1.4
-pancreas-case-study,pancreas-case-study.html,7
-loading-the-data,pancreas-case-study.html,7.1
-applying-the-annotation,pancreas-case-study.html,7.2
-diagnostics,pancreas-case-study.html,7.3
-comparison-to-clusters,pancreas-case-study.html,7.4
-fig:unref-pancreas-score-heatmap,pancreas-case-study.html,7.1
-fig:unref-pancreas-delta-dist,pancreas-case-study.html,7.2
-fig:unref-pancreas-marker-heat,pancreas-case-study.html,7.3
-fig:unref-pancreas-label-clusters,pancreas-case-study.html,7.4
-fig:unref-pancreas-label-tsne,pancreas-case-study.html,7.5
+pancreas-case-study,pancreas-case-study.html,8
+loading-the-data,pancreas-case-study.html,8.1
+applying-the-annotation,pancreas-case-study.html,8.2
+diagnostics,pancreas-case-study.html,8.3
+comparison-to-clusters,pancreas-case-study.html,8.4
+fig:unref-pancreas-score-heatmap,pancreas-case-study.html,8.1
+fig:unref-pancreas-delta-dist,pancreas-case-study.html,8.2
+fig:unref-pancreas-marker-heat,pancreas-case-study.html,8.3
+fig:unref-pancreas-label-clusters,pancreas-case-study.html,8.4
+fig:unref-pancreas-label-tsne,pancreas-case-study.html,8.5
 sc-mode,sc-mode.html,3
 overview-1,sc-mode.html,3.1
 annotation-with-test-based-marker-detection,sc-mode.html,3.2