"Gene set optimization for single cell transcriptomics" by H. Robert Frost

Resources

• Cell type-specific gene weights (as computed from the Human Protein Atlas Single Cell Type Atlas downloadable file rna_single_cell_type.tsv.zip): rna_single_cell_type_processed.csv.zip. This processed file adds the additional column 'FoldAboveMean' which contains the cell type-specific gene weights.
• Cell type-specific gene set weights for each of the Molecular Signature Database (MSigDB) collections (v2024.1). The MSigDB genes sets are publically available at https://www.gsea-msigdb.org/gsea/msigdb/index.jsp.
  • SetTestWeights_C1.tsv.zip
  • SetTestWeights_C2.CGP.tsv.zip
  • SetTestWeights_C2.CP.tsv.zip
  • SetTestWeights_C3.MIR.tsv.zip
  • SetTestWeights_C3.TFT.tsv.zip
  • SetTestWeights_C4.3CA.tsv.zip
  • SetTestWeights_C4.CGN.tsv.zip
  • SetTestWeights_C4.CM.tsv.zip
  • SetTestWeights_C5.GO.BP.tsv.zip
  • SetTestWeights_C5.GO.MF.tsv.zip
  • SetTestWeights_C5.HPO.tsv.zip
  • SetTestWeights_C6.tsv.zip
  • SetTestWeights_C7.IMMUNESIGDB.tsv.zip
  • SetTestWeights_C7.VAX.tsv.zip
  • SetTestWeights_C8.tsv.zip
• R logic that computes the results for the 10x PBMC3k scRNA-seq dataset included in the paper: PBMC3k_vignette.R. The PBMC scRNA-seq dataset is also used in the Seurat Guided Clustering Tutorial (https://satijalab.org/seurat/articles/pbmc3k_tutorial.html) and is freely accessible from 10x Genomics via a Creative Commons Attribution license at https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz.

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