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10-IntegrateScRNASeqHarmony_files/figure-gfm
10-IntegrateScRNASeqHarmony_files/figure-gfm
 
 
11-SeuratVignetteGuidedClustering_files/figure-gfm
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12-SeuratVignetteDataVisualization_files/figure-gfm
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13-SeuratVignetteSCTransform_files/figure-gfm
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14-SeuratVignetteMultimodalData_files/figure-gfm
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16-SeuratVignetteIntegration_files/figure-gfm
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17-SeuratVignetteMapping_files/figure-gfm
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18-SeuratVignetteBridge_files/figure-gfm
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19-SeuratVignetteWNN_files/figure-gfm
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2-VisualizeGeneExpression_files/figure-gfm
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20-SeuratVignetteSCRNAATAC_files/figure-gfm
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21-Phyloseq_files/figure-gfm
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22-Dada2pipeline_files/figure-gfm
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6-DeSeq2Workflow_files/figure-gfm
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7-IntegrateScRNASeqSeurat_files/figure-gfm
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8-DoubletFinder_files/figure-gfm
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9-RMAnormalizationMicroarray_files/figure-gfm
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RMD
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1-DownloadProcessDatasets.md
1-DownloadProcessDatasets.md
 
 
10-IntegrateScRNASeqHarmony.md
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11-SeuratVignetteGuidedClustering.md
11-SeuratVignetteGuidedClustering.md
 
 
12-SeuratVignetteDataVisualization.md
12-SeuratVignetteDataVisualization.md
 
 
13-SeuratVignetteSCTransform.md
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14-SeuratVignetteMultimodalData.md
14-SeuratVignetteMultimodalData.md
 
 
16-SeuratVignetteIntegration.md
16-SeuratVignetteIntegration.md
 
 
16.5-SeuratVignetteIntegrativeAnalysis.md
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17-SeuratVignetteMapping.Rmd
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17-SeuratVignetteMapping.md
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17-SeuratVignetteMapping.nb.html
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18-SeuratVignetteBridge.Rmd
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18-SeuratVignetteBridge.md
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19-SeuratVignetteWNN.Rmd
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19-SeuratVignetteWNN.md
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2-VisualizeGeneExpression.md
2-VisualizeGeneExpression.md
 
 
20-SeuratVignetteSCRNAATAC.Rmd
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20-SeuratVignetteSCRNAATAC.md
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21-Phyloseq.Rmd
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21-Phyloseq.md
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22-Dada2pipeline.Rmd
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22-Dada2pipeline.md
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3-ReadingDifferentFormatSingleCellData.md
3-ReadingDifferentFormatSingleCellData.md
 
 
4-RPKM-FPKM-TPM.md
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5-DeSeq2Intro.md
5-DeSeq2Intro.md
 
 
6-DeSeq2Workflow.md
6-DeSeq2Workflow.md
 
 
8-DoubletFinder.md
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9-RMAnormalizationMicroarray.md
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README.md
README.md
 
 

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BioinformaticsGuide

Hello this is my own practice studying NGS data analysis techniques using R and python.

Chapter 1. Download and Process Single Cell RNA Datasets

Chapter 2. Visualize Gene Expressions with R

Chapter 3. Reading Different formats of Single Cell Data using R and Seurat

Chapter 4. Understanding Normalization methods for Single Cell Data: RPKM, FPKM, TPM

Chapter 5. Introduction to DESeq2

Chapter 6. DESeq2 Workflow Tutorial

Chapter 7. Integrate Single Cell data with Seurat

The R Markdown link

Chapter 8. Using Doublet Finder

Chapter 9. DNA Microarray and using RMA normalization

Chapter 10. Integrate Single Cell data using Harmony

Chapter 11. Seurat Vignette - Guided Clustering

Chapter 12. Seurat Vignette - Data visualization

Chapter 13. Seurat Vignette - SCTransform

Chapter 14. Seurat Vignette - Multimodal analysis

Chapter 16. Seurat Vignette - scRNA-seq Integration

Chapter 17. Seurat Vignette - Mapping and Annotating query datasets

Chapter 18. Seurat Vignette - Bridge integration

Chapter 19. Seurat Vignette - Weighted Nearest Neighbors

Chapter 20. Seurat Vignette - Integrating scRNAseq and scATACseq

Chapter 21. Phyloseq - conducting microbiome studies

Chapter 22. Dada2 pipeline

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