https://github.com/fertiglab/geneoscollaboration

Repository for R code for single cell sequencing analysis published in Yarchoan, M., Gane, E.J., Marron, T.U. et al. Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial. Nat Med (2024).
https://github.com/fertiglab/geneoscollaboration

Last synced: 6 months ago
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Repository for R code for single cell sequencing analysis published in Yarchoan, M., Gane, E.J., Marron, T.U. et al. Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial. Nat Med (2024).

• Host: GitHub
• URL: https://github.com/fertiglab/geneoscollaboration
• Owner: FertigLab
• Created: 2023-07-05T16:46:41.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2024-04-08T12:53:07.000Z (about 2 years ago)
• Last Synced: 2025-10-25T15:42:48.937Z (8 months ago)
• Language: R
• Homepage: https://doi.org/10.1038/s41591-024-02894-y
• Size: 54.7 KB
• Stars: 7
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: readme.txt

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README

          
2024-02-16

This file provides explanation for the single cell RNA/TCR-seq data associated with the publication of the Phase I trial of GNOS-PV02 Personalized Neoantigen Vaccine, INO-9012 and Pembrolizumab in Subjects With Advanced HCC (NCT04251117). 

Pre-processed single cell data have been uploaded to the National Institutes of Health data repository Gene Expression Omnibus under the title "Gene expression and T cell repertoire profile at single cell level of peripheral blood T cells after treatment with a personalized neoantigen vaccine (GNOS-PV02) and Pembrolizumab for advanced hepatocellular carcinoma" (GSE255830). Original R code used to carry out the single cell sequencing analysis of these data have been uploaded to https://github.com/FertigLab/GeneosCollaboration.

Users wishing to re-analyze these data using the scripts shared on github should be aware of the following. In order to meet the upload requirements of GEO, unique filenames were created by appending a prefix to each of the pre-processed single cell RNA and TCR sequencing files (e.g. for Patient 6, "barcodes.tsv.gz" was renamed "GSM8081370_Pt__6_barcodes.tsv.gz", etc.). However, this is not the file format expected by the R scripts available on github. To make the files compatible with the R scripts, prefixes should be removed and all files corresponding to each patient must be placed in a unique folder named for the patient, as shown below:

data

  |- Pt_#6

  |- Pt_#7

  |- Pt_#8A

  |- Pt_#8B

Each subfolder should contain the following four files: "barcodes.tsv.gz", "features.tsv.gz", "filtered_contig_annotations.csv", "matrix.mtx.gz"