update

.Rproj.user/F5A33326/bookdown-crossref/03-step_by_step_scRNA_seq_pipeline.Rmd.xref

@@ -1,16 +1,53 @@
 h1:step-by-step-scrna-seq-pipeline Step-by-step scRNA-seq Pipeline
-h2:step-1.-load-the-r-packages-and-the-input-data Step 1. Load the R packages and the input data
+h2:before-you-begin Before you begin
+h2:step-1.-load-the-input-data Step 1. Load the input data
 h2:step-2.-quality-control Step 2. Quality Control
+h3:function-arguments Function arguments:
+h3:codes-for-running-step2 codes for running step2
+h3:outputs Outputs
 h2:step-3.-clustering Step 3. Clustering
 h2:step-4.-identify-cell-types Step 4. Identify Cell Types
+h3:codes-for-running-abccellmap codes for running abcCellmap
+h3:codes-for-running-the-cnv-analysis codes for running the CNV analysis
 h2:step-5.-visualization Step 5. Visualization
+h3:codes-for-peforming-three-dimensional-reduction-methods codes for peforming three dimensional reduction methods
+h3:codes-for-calculating-the-proportions codes for calculating the proportions
 h2:step-6.-find-degs Step 6. Find DEGs
+h3:codes-for-finding-degs codes for finding DEGs
+h3:codes-for-using-gptcelltype codes for using GPTCelltype
+h3:perform-go-and-kegg-enrichment. Perform GO and KEGG enrichment.
+h3:perform-subnetwork-analysis Perform subnetwork analysis
 h2:step-7.-assign-cell-cycles Step 7. Assign Cell Cycles
+h3:function-arguments-1 Function arguments:
+h3:codes-for-step7 codes for step7
+h3:outputs-1 Outputs
 h2:step-8.-calculate-heterogeneity Step 8. Calculate Heterogeneity
+h3:function-arguments-2 Function arguments:
+h3:codes-for-step8 codes for step8
 h2:step-9.-violin-plot-for-marker-genes Step 9. Violin Plot for Marker Genes
+h3:function-arguments-3 Function arguments:
+h3:codes-for-step9 codes for step9
 h2:step-10.-calculate-lineage-scores Step 10. Calculate Lineage Scores
+h3:function-arguments-4 Function arguments:
+h3:codes-for-step10 codes for step10
 h2:step-11.-gsva Step 11. GSVA
+h3:function-arguments-5 Function arguments:
+h3:codes-for-running-step11 codes for running step11
 h2:step-12.-construct-trajectories Step 12. Construct Trajectories
+h3:data-preparation data preparation
+h3:monocle2 monocle2
+h4:function-arguments-6 Function arguments:
+h4:codes-for-running-monocle2 codes for running monocle2
+h3:slingshot Slingshot
+h4:function-arguments-7 Function arguments:
+h4:codes-for-running-slingshot codes for running Slingshot
+h3:scvelo scVelo
+h4:function-arguments-8 Function arguments:
+h4:codes-for-running-scvelo codes for running Scvelo
 h2:step-13.-tf-analysis Step 13. TF Analysis
+h3:function-arguments-9 Function arguments:
+h3:codes-for-running-step13 codes for running step13
 h2:step-14.-cell-cell-interaction Step 14. Cell-Cell Interaction
+h3:function-arguments-10 Function arguments:
+h3:codes-for-running-step14 codes for running step14
 

.Rproj.user/shared/notebooks/paths

@@ -1,3 +1,2 @@
-D:/GitHub/HemaScope_Tutorial/HemaScope_installation_tutorial.Rmd="BD7D7C5F"
 D:/GitHub/HemaScope_Tutorial/_bookdown.yml="8A5771D1"
 D:/GitHub/HemaScope_Tutorial/_main.tex="09CE5142"

_book/reference-keys.txt

@@ -1,3 +1,35 @@
+fig:unnamed-chunk-15
+fig:unnamed-chunk-16
+fig:unnamed-chunk-17
+fig:unnamed-chunk-18
+fig:unnamed-chunk-20
+fig:unnamed-chunk-25
+fig:unnamed-chunk-32
+fig:unnamed-chunk-33
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+fig:unnamed-chunk-47
+fig:unnamed-chunk-51
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+fig:unnamed-chunk-96
+fig:unnamed-chunk-97
+fig:unnamed-chunk-101
+fig:unnamed-chunk-102
+fig:unnamed-chunk-103
 introduction
 installation
 create-a-new-conda-environment-and-activate-it
@@ -8,75 +40,112 @@ install-required-python-packages
 the-installed-packages-with-versions
 integrated-scrna-seq-pipeline
 step-by-step-scrna-seq-pipeline
-step-1.-load-the-r-packages-and-the-input-data
+before-you-begin
+step-1.-load-the-input-data
 step-2.-quality-control
+function-arguments
+codes-for-running-step2
+outputs
 step-3.-clustering
 step-4.-identify-cell-types
+codes-for-running-abccellmap
+codes-for-running-the-cnv-analysis
 step-5.-visualization
+codes-for-peforming-three-dimensional-reduction-methods
+codes-for-calculating-the-proportions
 step-6.-find-degs
+codes-for-finding-degs
+codes-for-using-gptcelltype
+perform-go-and-kegg-enrichment.
+perform-subnetwork-analysis
 step-7.-assign-cell-cycles
+function-arguments-1
+codes-for-step7
+outputs-1
 step-8.-calculate-heterogeneity
+function-arguments-2
+codes-for-step8
 step-9.-violin-plot-for-marker-genes
+function-arguments-3
+codes-for-step9
 step-10.-calculate-lineage-scores
+function-arguments-4
+codes-for-step10
 step-11.-gsva
+function-arguments-5
+codes-for-running-step11
 step-12.-construct-trajectories
+data-preparation
+monocle2
+function-arguments-6
+codes-for-running-monocle2
+slingshot
+function-arguments-7
+codes-for-running-slingshot
+scvelo
+function-arguments-8
+codes-for-running-scvelo
 step-13.-tf-analysis
+function-arguments-9
+codes-for-running-step13
 step-14.-cell-cell-interaction
+function-arguments-10
+codes-for-running-step14
 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
+function-arguments-11
 funciton-behavior
 an-example
-outputs
+outputs-2
 step-2.-qc
-function-arguments-1
+function-arguments-12
 function-behavior
 an-example-1
-outputs-1
+outputs-3
 step-3.-clustering-1
-function-arguments-2
+function-arguments-13
 function-behavior-1
 an-example-2
-outputs-2
+outputs-4
 step-4.-degs
-function-arguments-3
+function-arguments-14
 function-behavior-2
 an-example-3
-outputs-3
+outputs-5
 step-5.-spatially-variable-features
-function-arguments-4
+function-arguments-15
 function-behavior-3
 an-example-4
-outputs-4
+outputs-6
 step-6.-spatial-interaction
-function-arguments-5
+function-arguments-16
 function-behavior-4
 an-example-5
-outputs-5
+outputs-7
 step-7.-cnv-analysis
-function-arguments-6
+function-arguments-17
 function-behavior-5
 an-example-6
-outputs-6
+outputs-8
 step-8.-deconvolution
-function-arguments-7
+function-arguments-18
 function-behavior-6
 an-example-7
-outputs-7
+outputs-9
 step-9.-cell-cycle
-function-arguments-8
+function-arguments-19
 function-behavior-7
 an-example-8
-outputs-8
+outputs-10
 step-10.-niche-analysis
-function-arguments-9
+function-arguments-20
 function-behavior-8
 an-example-9
-outputs-9
+outputs-11
 step-by-step-shiny
 step-2.-load-the-r-packages-and-the-input-data
 step-3.-start-hemascopeshiny
@@ -109,134 +178,3 @@ 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
-fig:unnamed-chunk-12
-fig:unnamed-chunk-13
-fig:unnamed-chunk-14
-fig:unnamed-chunk-15
-step-1.-enter-r-and-get-the-path-of-the-installed-r-packages
-fig:unnamed-chunk-16
-fig:unnamed-chunk-21
-fig:unnamed-chunk-28
-fig:unnamed-chunk-29
-fig:unnamed-chunk-30
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-fig:unnamed-chunk-83
-fig:unnamed-chunk-85
-fig:unnamed-chunk-88
-fig:unnamed-chunk-93
-fig:unnamed-chunk-99
-before-you-begin
-step-1.-load-the-input-data
-parameters
-running-example
-codes-for-running-step1
-codes-for-running-step2
-function-arguments-10
-outputs-10
-codes-for-running-abccellmap
-run-the-cnv-copy-number-variation-analysis
-outputs-11
-outputs-12
-fig:unnamed-chunk-38
-fig:unnamed-chunk-41
-codes-for-running-the-cnv-analysis
-codes-for-running-step5
-section
-outputs-13
-codes-for-calculating-the-proportions
-codes-for-peforming-three-dimensional-reduction-methods
-outputs-14
-fig:unnamed-chunk-47
-codes-for-finding-degs
-codes-for-using-gptcelltype
-perform-go-and-kegg-enrichment.
-perform-subnetwork-analysis
-codes-for-step7
-codes-for-step8
-codes-for-step9
-codes-for-step10
-function-arguments-11
-function-arguments-12
-function-arguments-13
-function-arguments-14
-codes-for-running-step11
-data-preparation
-monocle2
-codes-for-running-monocle2
-slingshot
-function-arguments-15
-function-arguments-16
-codes-for-running-slingshot
-scvelo
-codes-for-running-scvelo
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-codes-for-running-step14
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