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Original R code used to carry out the single cell sequencing analysis of these data have been uploaded to https://github.com/FertigLab/GeneosCollaboration.\n\nUsers 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:\n\ndata\n  |- Pt_#6\n  |- Pt_#7\n  |- Pt_#8A\n  |- Pt_#8B\n\nEach subfolder should contain the following four files: \"barcodes.tsv.gz\", \"features.tsv.gz\", \"filtered_contig_annotations.csv\", \"matrix.mtx.gz\"\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffertiglab%2Fgeneoscollaboration","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffertiglab%2Fgeneoscollaboration","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffertiglab%2Fgeneoscollaboration/lists"}