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  "Title": "a novel tool for functional gene-set (or termed as pathway)\nanalysis of next-generation sequencing data",
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  "Date": "2021-11-21",
  "Author": "Xinan Yang <xyang2@uchicago.edu>; Bin Wang <binw@uchicago.edu>",
  "Maintainer": "Arjun Kinstlick <akinstlick@uchicago.edu>",
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  "Description": "Seq2pathway is a novel tool for functional gene-set (or\ntermed as pathway) analysis of next-generation sequencing data,\nconsisting of \"seq2gene\" and \"gene2path\" components. The\nseq2gene links sequence-level measurements of genomic regions\n(including SNPs or point mutation coordinates) to gene-level\nscores, and the gene2pathway summarizes gene scores to\npathway-scores for each sample. The seq2gene has the\nfeasibility to assign both coding and non-exon regions to a\nbroader range of neighboring genes than only the nearest one,\nthus facilitating the study of functional non-coding regions.\nThe gene2pathway takes into account the quantity of\nsignificance for gene members within a pathway compared those\noutside a pathway. The output of seq2pathway is a general\nstructure of quantitative pathway-level scores, thus allowing\none to functional interpret such datasets as RNA-seq, ChIP-seq,\nGWAS, and derived from other next generational sequencing\nexperiments.",
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