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ZhenyiWangTHU · Sep 29, 2024 · fa24cb2 · fa24cb2
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diff --git a/.../HemaScope_installation_tutorial.Rmd.xref → ...-HemaScope_installation_tutorial.Rmd.xref b/.../HemaScope_installation_tutorial.Rmd.xref → ...-HemaScope_installation_tutorial.Rmd.xref
diff --git a/...ef/integrated_scRNA_seq_pipeline.Rmd.xref → ...02-integrated_scRNA_seq_pipeline.Rmd.xref b/...ef/integrated_scRNA_seq_pipeline.Rmd.xref → ...02-integrated_scRNA_seq_pipeline.Rmd.xref
diff --git a/.../step_by_step_scRNA_seq_pipeline.Rmd.xref → ...-step_by_step_scRNA_seq_pipeline.Rmd.xref b/.../step_by_step_scRNA_seq_pipeline.Rmd.xref → ...-step_by_step_scRNA_seq_pipeline.Rmd.xref
diff --git a/.Rproj.user/F5A33326/bookdown-crossref/04-integrated_ST_pipeline.Rmd.xref b/.Rproj.user/F5A33326/bookdown-crossref/04-integrated_ST_pipeline.Rmd.xref
@@ -0,0 +1,5 @@
+h1:integrated-st-pipeline Integrated ST pipeline
+h2:for-10x-visium-data For 10X Visium data
+h2:for-merfish-data For MERFISH data
+h2:for-stereo-seq-data For stereo-seq data
+
diff --git a/...ref/step_by_step_st_seq_pipeline.Rmd.xref → .../05-step_by_step_st_seq_pipeline.Rmd.xref b/...ref/step_by_step_st_seq_pipeline.Rmd.xref → .../05-step_by_step_st_seq_pipeline.Rmd.xref
diff --git a/...down-crossref/step_by_step_shiny.Rmd.xref → ...n-crossref/06-step_by_step_shiny.Rmd.xref b/...down-crossref/step_by_step_shiny.Rmd.xref → ...n-crossref/06-step_by_step_shiny.Rmd.xref
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diff --git a/.Rproj.user/F5A33326/sources/prop/INDEX b/.Rproj.user/F5A33326/sources/prop/INDEX
@@ -1,2 +1,4 @@
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+D%3A%2FGitHub%2FHemaScope_Tutorial%2F_bookdown.yml="18B719A4"
+D%3A%2FGitHub%2FHemaScope_Tutorial%2F_main.tex="DCDE526A"
diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
@@ -1,2 +1,3 @@
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 D:/GitHub/HemaScope_Tutorial/HemaScope_installation_tutorial.Rmd="BD7D7C5F"
+D:/GitHub/HemaScope_Tutorial/_bookdown.yml="8A5771D1"
+D:/GitHub/HemaScope_Tutorial/_main.tex="09CE5142"
diff --git a/HemaScope_installation_tutorial.Rmd → 01-HemaScope_installation_tutorial.Rmd b/HemaScope_installation_tutorial.Rmd → 01-HemaScope_installation_tutorial.Rmd
diff --git a/integrated_scRNA_seq_pipeline.Rmd → 02-integrated_scRNA_seq_pipeline.Rmd b/integrated_scRNA_seq_pipeline.Rmd → 02-integrated_scRNA_seq_pipeline.Rmd
diff --git a/step_by_step_scRNA_seq_pipeline.Rmd → 03-step_by_step_scRNA_seq_pipeline.Rmd b/step_by_step_scRNA_seq_pipeline.Rmd → 03-step_by_step_scRNA_seq_pipeline.Rmd
diff --git a/integrated_ST_pipeline.Rmd → 04-integrated_ST_pipeline.Rmd b/integrated_ST_pipeline.Rmd → 04-integrated_ST_pipeline.Rmd
diff --git a/step_by_step_st_seq_pipeline.Rmd → 05-step_by_step_st_seq_pipeline.Rmd b/step_by_step_st_seq_pipeline.Rmd → 05-step_by_step_st_seq_pipeline.Rmd
diff --git a/step_by_step_shiny.Rmd → 06-step_by_step_shiny.Rmd b/step_by_step_shiny.Rmd → 06-step_by_step_shiny.Rmd
diff --git a/HemaScope_Tutorial.Rmd b/HemaScope_Tutorial.Rmd
diff --git a/_book/image/radian.png b/_book/image/radian.png
diff --git a/_book/image/sc_shiny_images/sc_page.png b/_book/image/sc_shiny_images/sc_page.png
diff --git a/_book/image/sc_shiny_images/sc_step1.png b/_book/image/sc_shiny_images/sc_step1.png
diff --git a/_book/image/sc_shiny_images/sc_step10.png b/_book/image/sc_shiny_images/sc_step10.png
diff --git a/_book/image/sc_shiny_images/sc_step11.png b/_book/image/sc_shiny_images/sc_step11.png
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diff --git a/_book/image/sc_shiny_images/sc_step13.png b/_book/image/sc_shiny_images/sc_step13.png
diff --git a/_book/image/sc_shiny_images/sc_step14.png b/_book/image/sc_shiny_images/sc_step14.png
diff --git a/_book/image/sc_shiny_images/sc_step15.png b/_book/image/sc_shiny_images/sc_step15.png
diff --git a/_book/image/sc_shiny_images/sc_step2.png b/_book/image/sc_shiny_images/sc_step2.png
diff --git a/_book/image/sc_shiny_images/sc_step3.png b/_book/image/sc_shiny_images/sc_step3.png
diff --git a/_book/image/sc_shiny_images/sc_step4.png b/_book/image/sc_shiny_images/sc_step4.png
diff --git a/_book/image/sc_shiny_images/sc_step5.png b/_book/image/sc_shiny_images/sc_step5.png
diff --git a/_book/image/sc_shiny_images/sc_step6.png b/_book/image/sc_shiny_images/sc_step6.png
diff --git a/_book/image/sc_shiny_images/sc_step7.png b/_book/image/sc_shiny_images/sc_step7.png
diff --git a/_book/image/sc_shiny_images/sc_step8.png b/_book/image/sc_shiny_images/sc_step8.png
diff --git a/_book/image/sc_shiny_images/sc_step9.png b/_book/image/sc_shiny_images/sc_step9.png
diff --git a/_book/image/shiny.png b/_book/image/shiny.png
diff --git a/_book/image/shiny_UI.png b/_book/image/shiny_UI.png
diff --git a/_book/image/shiny_home.png b/_book/image/shiny_home.png
diff --git a/_book/image/st_shiny_images/st_step1.png b/_book/image/st_shiny_images/st_step1.png
diff --git a/_book/image/st_shiny_images/st_step2.png b/_book/image/st_shiny_images/st_step2.png
diff --git a/_book/image/st_shiny_images/st_step3.png b/_book/image/st_shiny_images/st_step3.png
diff --git a/_book/image/st_shiny_images/st_step4.png b/_book/image/st_shiny_images/st_step4.png
diff --git a/_book/image/st_shiny_images/st_step5.png b/_book/image/st_shiny_images/st_step5.png
diff --git a/_book/image/st_shiny_images/st_step6.png b/_book/image/st_shiny_images/st_step6.png
diff --git a/_book/image/st_shiny_images/st_step7.png b/_book/image/st_shiny_images/st_step7.png
diff --git a/_book/image/web_home.png b/_book/image/web_home.png
diff --git a/_book/index.html b/_book/index.html
diff --git a/_book/installation.html b/_book/installation.html
diff --git a/_book/integrated-scrna-seq-pipeline.html b/_book/integrated-scrna-seq-pipeline.html
diff --git a/_book/integrated-st-pipeline.html b/_book/integrated-st-pipeline.html
diff --git a/_book/reference-keys.txt b/_book/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/_book/search_index.json b/_book/search_index.json