{
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  "Package": "atSNP",
  "Type": "Package",
  "Title": "Affinity test for identifying regulatory SNPs",
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  "Date": "2021-4-26",
  "Authors@R": "c(person(given = \"Chandler\", family = \"Zuo\", role = \"aut\"),\nperson(given = \"Sunyoung\",family = \"Shin\",role = c(\"aut\", \"cre\"), email = \"sunyoung.shin@utdallas.edu\"),\nperson(given = \"Sunduz\", family = \"Keles\", role = \"aut\"))",
  "Description": "atSNP performs affinity tests of motif matches with the\nSNP or the reference genomes and SNP-led changes in motif\nmatches.",
  "License": "GPL-2",
  "RoxygenNote": "6.1.1",
  "biocViews": "Software, ChIPSeq, GenomeAnnotation, MotifAnnotation,\nVisualization",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:34 UTC",
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  "Author": "Chandler Zuo [aut],\nSunyoung Shin [aut, cre],\nSunduz Keles [aut]",
  "Maintainer": "Sunyoung Shin <sunyoung.shin@utdallas.edu>",
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        "ref_strand",
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        "IUPAC",
        "ref_match_seq",
        "snp_match_seq",
        "ref_seq_snp_match",
        "snp_seq_ref_match",
        "snpbase",
        "snp_ref_start",
        "snp_ref_end",
        "snp_ref_length",
        "ref_aug_match_seq_forward",
        "ref_aug_match_seq_reverse",
        "snp_aug_match_seq_forward",
        "snp_aug_match_seq_reverse",
        "ref_location",
        "snp_location",
        "ref_extra_pwm_left",
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      "tojson": true
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      "tojson": true
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    {
      "page": "atSNP-package",
      "title": "atSNP: affinity tests for regulatory SNP detection",
      "topics": [
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      ]
    },
    {
      "page": "ComputeMotifScore",
      "title": "Compute the scores for SNP effects on motifs.",
      "topics": [
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    {
      "page": "ComputePValues",
      "title": "Compute p-values for affinity scores.",
      "topics": [
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    },
    {
      "page": "dtMotifMatch",
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      "topics": [
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      "topics": [
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    },
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    {
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      "title": "A motif library containing 593 motifs downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.",
      "topics": [
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      "page": "jaspar_motifinfo",
      "title": "The information for the motif library downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.",
      "topics": [
        "jaspar_motifinfo"
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      "title": "Load the SNP data from fasta files.",
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      "page": "LoadMotifLibrary",
      "title": "Load position weight matrices.",
      "topics": [
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    },
    {
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      "title": "Load the SNP information and code the genome sequences around the SNP locations.",
      "topics": [
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      "title": "Compute the matching subsequence.",
      "topics": [
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      "title": "Composit logo plotting input containing motif scores, the matching subsequences and the augmented matching subsequences on SNP and reference allele",
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      "topics": [
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    },
    {
      "page": "plotMotifMatch",
      "title": "Plot sequence logos of the position weight matrix of the motif and sequences of its corresponding best matching augmented subsequence on the reference and SNP allele.",
      "topics": [
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    },
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  "_vignettes": [
    {
      "source": "atsnp-vignette.rmd",
      "filename": "atsnp-vignette.html",
      "title": "atSNP: affinity tests for regulatory SNP detection",
      "author": "Chandler Zuo, Sunyoung Shin, Sunduz Keles",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Example",
        "Load the motif library",
        "ENCODE derived motif library",
        "JASPAR database motif library",
        "User defined motif library",
        "Load the SNP Data",
        "Load SNP data through a table",
        "Load SNP data through dbSNP's rsids",
        "Load SNP data through a pair of fasta files",
        "Affinity score tests",
        "Load the example data",
        "Compute affinity scores",
        "Compute p-values",
        "Multiple testing adjustment",
        "Additional analysis",
        "Session Information"
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      "created": "2018-12-29 09:27:24",
      "modified": "2021-04-26 23:15:40",
      "commits": 19
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