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ZhenyiWangTHU · Sep 29, 2024 · d1d9bcf · d1d9bcf
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diff --git a/docs/image/radian.png b/docs/image/radian.png
diff --git a/docs/image/sc_shiny_images/sc_page.png b/docs/image/sc_shiny_images/sc_page.png
diff --git a/docs/image/sc_shiny_images/sc_step1.png b/docs/image/sc_shiny_images/sc_step1.png
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diff --git a/docs/image/sc_shiny_images/sc_step13.png b/docs/image/sc_shiny_images/sc_step13.png
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diff --git a/docs/image/sc_shiny_images/sc_step15.png b/docs/image/sc_shiny_images/sc_step15.png
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diff --git a/docs/image/sc_shiny_images/sc_step3.png b/docs/image/sc_shiny_images/sc_step3.png
diff --git a/docs/image/sc_shiny_images/sc_step4.png b/docs/image/sc_shiny_images/sc_step4.png
diff --git a/docs/image/sc_shiny_images/sc_step5.png b/docs/image/sc_shiny_images/sc_step5.png
diff --git a/docs/image/sc_shiny_images/sc_step6.png b/docs/image/sc_shiny_images/sc_step6.png
diff --git a/docs/image/sc_shiny_images/sc_step7.png b/docs/image/sc_shiny_images/sc_step7.png
diff --git a/docs/image/sc_shiny_images/sc_step8.png b/docs/image/sc_shiny_images/sc_step8.png
diff --git a/docs/image/sc_shiny_images/sc_step9.png b/docs/image/sc_shiny_images/sc_step9.png
diff --git a/docs/image/shiny.png b/docs/image/shiny.png
diff --git a/docs/image/shiny_UI.png b/docs/image/shiny_UI.png
diff --git a/docs/image/shiny_home.png b/docs/image/shiny_home.png
diff --git a/docs/image/st_shiny_images/st_step1.png b/docs/image/st_shiny_images/st_step1.png
diff --git a/docs/image/st_shiny_images/st_step2.png b/docs/image/st_shiny_images/st_step2.png
diff --git a/docs/image/st_shiny_images/st_step3.png b/docs/image/st_shiny_images/st_step3.png
diff --git a/docs/image/st_shiny_images/st_step4.png b/docs/image/st_shiny_images/st_step4.png
diff --git a/docs/image/st_shiny_images/st_step5.png b/docs/image/st_shiny_images/st_step5.png
diff --git a/docs/image/st_shiny_images/st_step6.png b/docs/image/st_shiny_images/st_step6.png
diff --git a/docs/image/st_shiny_images/st_step7.png b/docs/image/st_shiny_images/st_step7.png
diff --git a/docs/image/web_home.png b/docs/image/web_home.png
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/installation.html b/docs/installation.html
diff --git a/docs/integrated-scrna-seq-pipeline.html b/docs/integrated-scrna-seq-pipeline.html
diff --git a/docs/integrated-st-pipeline.html b/docs/integrated-st-pipeline.html
diff --git a/docs/reference-keys.txt b/docs/reference-keys.txt
@@ -22,6 +22,10 @@ step-11.-gsva
 step-12.-construct-trajectories
 step-13.-tf-analysis
 step-14.-cell-cell-interaction
+integrated-st-pipeline
+for-10x-visium-data
+for-merfish-data
+for-stereo-seq-data
 stey-by-step-st-seq-pipeline
 step-1.-data-loading
 function-arguments
@@ -73,3 +77,35 @@ function-arguments-9
 function-behavior-8
 an-example-9
 outputs-9
+step-by-step-shiny
+step-2.-load-the-r-packages-and-the-input-data
+step-3.-start-hemascopeshiny
+step-4.-use-hemascopeshiny-via-the-gui
+scrna-seq-pipeline
+step-1-scrna-seq-pipeline.-input-data
+step-2-scrna-seq-pipeline.-quality-control
+step-3-scrna-seq-pipeline.-clustering
+step-4-scrna-seq-pipeline.-identify-cell-types
+step-5-scrna-seq-pipeline.-visualization
+step-6-scrna-seq-pipeline.-find-differential-genes
+step-7-scrna-seq-pipeline.-assign-cell-cycles
+step-8-scrna-seq-pipeline.-calculate-heterogeneity
+step-9-scrna-seq-pipeline.-violin-plot-for-marker-genes
+step-10-scrna-seq-pipeline.-calculate-lineage-scores
+step-11-scrna-seq-pipeline.-gsva
+step-12-scrna-seq-pipeline.-construct-trajectories
+step-13-scrna-seq-pipeline.-transcription-factors-analysis
+step-14-scrna-seq-pipeline.-cell-cell-interaction
+step-15-scrna-seq-pipeline.-generate-the-report
+st-pipeline
+step-1-st-seq-pipeline.-input-data
+step-2-st-seq-pipeline.-quality-control
+step-3-st-seq-pipeline.-clustering
+step-4-st-seq-pipeline.-find-differential-genes
+step-5-st-seq-pipeline.-spatially-variable-features
+step-6-st-seq-pipeline.-spatial-interaction
+step-7-st-seq-pipeline.-cnv-analysis
+step-8-st-seq-pipeline.-deconvolution
+step-9-st-seq-pipeline.-cell-cycle-analysis
+step-10-st-seq-pipeline.-niche-analysis
+step-11-st-seq-pipeline.-generate-the-report
diff --git a/docs/search_index.json b/docs/search_index.json
diff --git a/docs/step-by-step-scrna-seq-pipeline.html b/docs/step-by-step-scrna-seq-pipeline.html
diff --git a/docs/step-by-step-shiny.html b/docs/step-by-step-shiny.html
diff --git a/docs/stey-by-step-st-seq-pipeline.html b/docs/stey-by-step-st-seq-pipeline.html