Update README.md

README.md

@@ -10,23 +10,23 @@ R code files are located in parent directory. These files should be executed in
 /code_inputs/: Processed data objects loaded and used in at least one of the R code files. Currently not available due to data sharing permissions, but will be uploaded to dbGaP and appropriate repositories. 
 ## Scope of Analysis Scripts
 The contents of this repo include: 
-
-I. QC and annotation of single-cell RNA data for 5 subjects receiving mKRAS-Vax. Isolation of annotated T cells from single-cell data. 
-		A.2023_05_29_Read10x.r: Process CellRanger output into aggregate Seurat object.
-		B.2023_06_06_sc-by-batch.r: Split aggregate object by sequencing batch. Perform separate QC and filtering. 
-		C.2023_11_08_sc-cluster-assignment-batch1.r: Annotate putative T cell clusters based on cluster markers and Azimuth annotation for sequencing batch 1. 
-		D.2023_11_08_sc-cluster-assignment-batch2.r: Annotate putative T cell clusters based on cluster markers and Azimuth annotation for sequencing batch 2. 
-II. Analysis of T-cell expansion assays to identify clonotypes expanded to mKRAS peptides. 
-		E.2023_05_05_DiffExFESTData.r: Analyze expansion assay data to identify T cell receptor clonotypes expanded to mKRAS peptides. 
-		F.2024_04_18_MakeFilteredDiffExTable.r: Generate compiled table of all mKRAS expanded TCRs 
-III. Integration of single-cell and TCR expansion data to identify anti-mKRAS T cells in single-cell data. 
-		G.2024_04_17_scKRASAnnot.r: Integrate mKRAS expansion data and single-cell data to create a new Seurat object with annotations for anti-mKRAS T cell reactivity. 
-		H.2024_05_08_pullAllmKRAS_withExpansionInfo-all.r: Generate composite table containing paired chain information, T cell phenotype, and mKRAS reactivity for anti-mKRAS TCRs in scRNA data.
-		I.2024_04_27_MinorEditingObjects.r: Combine annotated T cell objects for batch 1 and batch2 back into one seurat object for convenience. 
-IV. Analysis of gene expression profile of mKRAS-specific T-cells. 
-		J.2024-04-23_Seurat_viz.Rmd
-V. Comparison of mKRAS TCRs with TCGA data. 
-		K.024-04-29_TCGA.Rmd
+1. QC and annotation of single-cell RNA data for 5 subjects receiving mKRAS-Vax. Isolation of annotated T cells from single-cell data.
+   - A.2023_05_29_Read10x.r: Process CellRanger output into aggregate Seurat object.
+   - B.2023_06_06_sc-by-batch.r: Split aggregate object by sequencing batch. Perform separate QC and filtering.
+   - C.2023_11_08_sc-cluster-assignment-batch1.r: Annotate putative T cell clusters based on cluster markers and Azimuth annotation for sequencing batch 1.
+   - D.2023_11_08_sc-cluster-assignment-batch2.r: Annotate putative T cell clusters based on cluster markers and Azimuth annotation for sequencing batch 2.
+2. Analysis of T-cell expansion assays to identify clonotypes expanded to mKRAS peptides.
+   - E.2023_05_05_DiffExFESTData.r: Analyze expansion assay data to identify T cell receptor clonotypes expanded to mKRAS peptides. 
+   - F.2024_04_18_MakeFilteredDiffExTable.r: Generate compiled table of all mKRAS expanded TCRs
+3. Integration of single-cell and TCR expansion data to identify anti-mKRAS T cells in single-cell data. 
+   - G.2024_04_17_scKRASAnnot.r: Integrate mKRAS expansion data and single-cell data to create a new Seurat object with annotations for anti-mKRAS T cell reactivity. 
+   - H.2024_05_08_pullAllmKRAS_withExpansionInfo-all.r: Generate composite table containing paired chain information, T cell phenotype, and mKRAS reactivity for anti-mKRAS TCRs in scRNA data.
+   - I.2024_04_27_MinorEditingObjects.r: Combine annotated T cell objects for batch 1 and batch2 back into one seurat object for convenience. 
+4. Analysis of gene expression profile of mKRAS-specific T-cells. 
+   - J.2024-04-23_Seurat_viz.Rmd
+5. Comparison of mKRAS TCRs with TCGA data.
+   - K.024-04-29_TCGA.Rmd
+     
 ## Other Files
 		LICENSE: GNU v3.0 license governing the use and sharing of code in this repository. 
 		SESSIONINFO: R Package versions for libraries used in analysis scripts for I-III described above.