Add data, tools, and learning objectives.

Collapse PCA output.
stevenjm11 · Nov 18, 2024 · a6d3d28 · a6d3d28
1 parent 4ce7404
commit a6d3d28
Showing 1 changed file with 54 additions and 38 deletions.
diff --git a/docs/tutorials/seurat-go/seurat-go.md b/docs/tutorials/seurat-go/seurat-go.md
@@ -22,16 +22,27 @@
 * [x] Intermediate  
 * [ ] Advanced  
 
-**Data:** Placeholder.
+**Data:** 10k Human PBMCs, Multiome v1.0, Chromium X.
 
-**Tools:** Placeholder.
+**Tools:** R >= 4.4.0 and associated packages:  
+
+- Seurat  
+- SeuratData  
+- clusterProfiler  
+- Signac  
+- ggplot2  
 
 **Pipeline:**  
 *Section 1:* Setup, Introduction, and Preprocessing.  
 *Section 2:* Gene Ontology analysis.  
 *Section 3:* Integration of ATAC-seq data.  
 
-**Learning objectives:** Placeholder.
+**Learning objectives:**  
+
+- Apply GO enrichment analysis to identify biological processes, molecular functions, and cellular components represented in single-cell RNA-seq data.  
+- Interpret GO results and identify key pathways and functional modules relevant to specific biological questions.  
+- Design a workflow for integrating various omics layers, considering the biological context and research goals.  
+- Take advantage of the Seurat, Signac and clusterProfiler R packages to perform the analysis, generate plots and interpret the results.  
 
 <!--
 !!! warning "Disclaimer"
@@ -156,43 +167,48 @@ pbmc.rna <- ScaleData(pbmc.rna)
 ## Centering and scaling data matrix
 
 pbmc.rna <- RunPCA(pbmc.rna)
+```
 
-## PC_ 1 
-## Positive:  PLXDC2, SLC8A1, LRMDA, FCN1, TYMP, MCTP1, JAK2, RBM47, IRAK3, NAMPT 
-##     DMXL2, TBXAS1, ZEB2, LYN, LRRK2, SAT1, GAB2, CYBB, TNFAIP2, CSF3R 
-##     HCK, TLR2, CLEC7A, LYST, VCAN, DENND1A, FGD4, CD36, GRK3, FAM49A 
-## Negative:  CD247, IL32, CAMK4, IL7R, LTB, LEF1, BACH2, INPP4B, BCL2, SYNE2 
-##     THEMIS, TRBC2, RORA, TXK, ANK3, CD69, TRBC1, MLLT3, APBA2, ACTG1 
-##     RASGRF2, NELL2, LINC01934, TAFA1, SAMD3, PCAT1, PFN1, NCALD, CTSW, KCNQ5 
-## PC_ 2 
-## Positive:  CD247, IL32, DPYD, IL7R, INPP4B, AOAH, CAMK4, PDE3B, THEMIS, TXK 
-##     RORA, LEF1, SLCO3A1, NEAT1, FNDC3B, ARHGAP26, ANXA1, SRGN, ADGRE5, SAMD3 
-##     SYNE2, NCALD, TRBC1, CTSW, PLCB1, APBA2, CCL5, S100A4, TGFBR3, PRF1 
-## Negative:  BANK1, PAX5, MS4A1, FCRL1, NIBAN3, AFF3, IGHM, EBF1, LINC00926, OSBPL10 
-##     RALGPS2, CD79A, CD22, COBLL1, BLK, BLNK, AP002075.1, ADAM28, IGHD, COL19A1 
-##     BCL11A, CD79B, PLEKHG1, GNG7, DENND5B, WDFY4, TCF4, AC120193.1, RUBCNL, SPIB 
-## PC_ 3 
-## Positive:  BACH2, LEF1, PDE3B, CAMK4, IL7R, LTB, ANK3, FHIT, INPP4B, NELL2 
-##     BCL2, RASGRF2, CSGALNACT1, SLC2A3, MLLT3, AC139720.1, PLCL1, PRKN, PAX5, FCRL1 
-##     LINC00926, TSHZ2, MS4A1, PTPRK, AL589693.1, CD79A, EBF1, ST6GALNAC3, BANK1, COL19A1 
-## Negative:  GZMB, NKG7, GNLY, PRF1, KLRD1, GZMA, CST7, CLIC3, CCL5, FGFBP2 
-##     SPON2, ADGRG1, KLRF1, GZMH, CCL4, TGFBR3, LINC00996, LINC01478, PDGFD, PTGDR 
-##     C1orf21, FCRL6, CLEC4C, SLAMF7, BNC2, CTSW, IL2RB, EPHB1, LILRA4, HOPX 
-## PC_ 4 
-## Positive:  NKG7, GNLY, PRF1, KLRD1, GZMA, CST7, CCL5, FGFBP2, MCTP2, ADGRG1 
-##     GZMH, CCL4, KLRF1, FCGR3A, SPON2, TGFBR3, PDGFD, PAX5, FCRL1, MS4A1 
-##     FCRL6, PTGDR, BNC2, MTSS1, CX3CR1, LINC00926, C1orf21, IL2RB, PPP2R2B, HOPX 
-## Negative:  LINC01478, CUX2, EPHB1, CLEC4C, LILRA4, COL26A1, AC023590.1, PTPRS, SCN9A, LINC01374 
-##     COL24A1, LINC00996, NRP1, PHEX, FAM160A1, TNFRSF21, PLXNA4, PACSIN1, SCAMP5, SLC35F3 
-##     DNASE1L3, P3H2, LRRC26, PLD4, ITM2C, SCN1A-AS1, PLEKHD1, SERPINF1, SCT, PTCRA 
-## PC_ 5 
-## Positive:  CDKN1C, IFITM3, HES4, CSF1R, SMIM25, FCGR3A, MS4A7, LST1, AIF1, LRRC25 
-##     AC104809.2, MAFB, CALHM6, CFD, AC020651.2, SERPINA1, GPBAR1, SIGLEC10, CST3, HMOX1 
-##     CTSL, TCF7L2, FMNL2, HLA-DPA1, CKB, MTSS1, COTL1, IFI30, CCDC26, SPRED1 
-## Negative:  PLCB1, VCAN, ARHGAP24, CSF3R, DYSF, LINC00937, FNDC3B, GLT1D1, VCAN-AS1, AC020916.1 
-##     PDE4D, PADI4, ARHGAP26, CREB5, TREM1, MCTP2, CD36, MEGF9, KIF13A, MICAL2 
-##     FCAR, ACSL1, CLMN, JUN, ANXA1, MIR646HG, RAB11FIP1, CRISPLD2, GNLY, ZBTB16
+??? note "Output"
+    ```r
+    ## PC_ 1 
+    ## Positive:  PLXDC2, SLC8A1, LRMDA, FCN1, TYMP, MCTP1, JAK2, RBM47, IRAK3, NAMPT 
+    ##     DMXL2, TBXAS1, ZEB2, LYN, LRRK2, SAT1, GAB2, CYBB, TNFAIP2, CSF3R 
+    ##     HCK, TLR2, CLEC7A, LYST, VCAN, DENND1A, FGD4, CD36, GRK3, FAM49A 
+    ## Negative:  CD247, IL32, CAMK4, IL7R, LTB, LEF1, BACH2, INPP4B, BCL2, SYNE2 
+    ##     THEMIS, TRBC2, RORA, TXK, ANK3, CD69, TRBC1, MLLT3, APBA2, ACTG1 
+    ##     RASGRF2, NELL2, LINC01934, TAFA1, SAMD3, PCAT1, PFN1, NCALD, CTSW, KCNQ5 
+    ## PC_ 2 
+    ## Positive:  CD247, IL32, DPYD, IL7R, INPP4B, AOAH, CAMK4, PDE3B, THEMIS, TXK 
+    ##     RORA, LEF1, SLCO3A1, NEAT1, FNDC3B, ARHGAP26, ANXA1, SRGN, ADGRE5, SAMD3 
+    ##     SYNE2, NCALD, TRBC1, CTSW, PLCB1, APBA2, CCL5, S100A4, TGFBR3, PRF1 
+    ## Negative:  BANK1, PAX5, MS4A1, FCRL1, NIBAN3, AFF3, IGHM, EBF1, LINC00926, OSBPL10 
+    ##     RALGPS2, CD79A, CD22, COBLL1, BLK, BLNK, AP002075.1, ADAM28, IGHD, COL19A1 
+    ##     BCL11A, CD79B, PLEKHG1, GNG7, DENND5B, WDFY4, TCF4, AC120193.1, RUBCNL, SPIB 
+    ## PC_ 3 
+    ## Positive:  BACH2, LEF1, PDE3B, CAMK4, IL7R, LTB, ANK3, FHIT, INPP4B, NELL2 
+    ##     BCL2, RASGRF2, CSGALNACT1, SLC2A3, MLLT3, AC139720.1, PLCL1, PRKN, PAX5, FCRL1 
+    ##     LINC00926, TSHZ2, MS4A1, PTPRK, AL589693.1, CD79A, EBF1, ST6GALNAC3, BANK1, COL19A1 
+    ## Negative:  GZMB, NKG7, GNLY, PRF1, KLRD1, GZMA, CST7, CLIC3, CCL5, FGFBP2 
+    ##     SPON2, ADGRG1, KLRF1, GZMH, CCL4, TGFBR3, LINC00996, LINC01478, PDGFD, PTGDR 
+    ##     C1orf21, FCRL6, CLEC4C, SLAMF7, BNC2, CTSW, IL2RB, EPHB1, LILRA4, HOPX 
+    ## PC_ 4 
+    ## Positive:  NKG7, GNLY, PRF1, KLRD1, GZMA, CST7, CCL5, FGFBP2, MCTP2, ADGRG1 
+    ##     GZMH, CCL4, KLRF1, FCGR3A, SPON2, TGFBR3, PDGFD, PAX5, FCRL1, MS4A1 
+    ##     FCRL6, PTGDR, BNC2, MTSS1, CX3CR1, LINC00926, C1orf21, IL2RB, PPP2R2B, HOPX 
+    ## Negative:  LINC01478, CUX2, EPHB1, CLEC4C, LILRA4, COL26A1, AC023590.1, PTPRS, SCN9A, LINC01374 
+    ##     COL24A1, LINC00996, NRP1, PHEX, FAM160A1, TNFRSF21, PLXNA4, PACSIN1, SCAMP5, SLC35F3 
+    ##     DNASE1L3, P3H2, LRRC26, PLD4, ITM2C, SCN1A-AS1, PLEKHD1, SERPINF1, SCT, PTCRA 
+    ## PC_ 5 
+    ## Positive:  CDKN1C, IFITM3, HES4, CSF1R, SMIM25, FCGR3A, MS4A7, LST1, AIF1, LRRC25 
+    ##     AC104809.2, MAFB, CALHM6, CFD, AC020651.2, SERPINA1, GPBAR1, SIGLEC10, CST3, HMOX1 
+    ##     CTSL, TCF7L2, FMNL2, HLA-DPA1, CKB, MTSS1, COTL1, IFI30, CCDC26, SPRED1 
+    ## Negative:  PLCB1, VCAN, ARHGAP24, CSF3R, DYSF, LINC00937, FNDC3B, GLT1D1, VCAN-AS1, AC020916.1 
+    ##     PDE4D, PADI4, ARHGAP26, CREB5, TREM1, MCTP2, CD36, MEGF9, KIF13A, MICAL2 
+    ##     FCAR, ACSL1, CLMN, JUN, ANXA1, MIR646HG, RAB11FIP1, CRISPLD2, GNLY, ZBTB16
+    ```
 
+```r
 pbmc.rna <- RunUMAP(pbmc.rna, dims = 1:30)
 
 ## Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric