This repository contains processed data and analysis scripts used in the manuscript by Huff et. al, "An off-the-shelf vaccine activates a broad repertoire of mutant KRAS-specific T cells in patients with resected pancreatic cancer". Code written by Alexander Girgis and Ludmila Danilova.
R code files are located in parent directory. These files should be executed in their current location relative to all subfolders in directory.
/code_outputs/: Empty folder which will become populated with resluts files upon executing R code files. /_rfunctions/: Code folder contaning miscellaneous helper functions in processing TRBV nomenclature. /raw_data/: Contains scRNA and scVDJ output from CellRanger pipeline. Currently not available due to data sharing permissions, but will be uploaded to dbGaP and appropriate repositories. /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.
The contents of this repo include:
- 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.
- 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
- 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.
- Analysis of gene expression profile of mKRAS-specific T-cells.
- J.2024-04-23_Seurat_viz.Rmd
- Comparison of mKRAS TCRs with TCGA data.
- K.024-04-29_TCGA.Rmd
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.