Skip to content

scRNA and TCR analysis, including T-cell expansion assays, from subjects in J1994 manuscript by Huff et al.

License

Notifications You must be signed in to change notification settings

FertigLab/mKRAS-Vax

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

4 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

J1994.scRNA-TCR

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.

Directory Structure

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.

Scope of Analysis Scripts

The contents of this repo include:

  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. 

About

scRNA and TCR analysis, including T-cell expansion assays, from subjects in J1994 manuscript by Huff et al.

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Languages