{
  "_id": "6aca22fffe5cc25786e850aa",
  "Package": "AssessORFData",
  "Type": "Package",
  "Title": "Data and Files for the AssessORF Package",
  "Version": "1.30.0",
  "Date": "2019-04-07",
  "Authors@R": "c(\nperson(\"Deepank\", \"Korandla\", email = \"dkorandl@alumni.cmu.edu\", role = \"aut\"),\nperson(\"Nicholas\", \"Cooley\", email = \"npc19@pitt.edu\", role = \"cre\", comment = c(ORCID = \"0000-0002-6029-304X\")))",
  "Description": "This package provides access to mapping and results\nobjects generated by the AssessORF package, as well as the\ngenome sequences for the strains corresponding to those\nobjects.",
  "biocViews": "OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data,\nPseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data,\nGenome, Proteome, SequencingData",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "FALSE",
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  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:32:20 UTC",
  "RemoteUrl": "https://github.com/bioc/AssessORFData",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "ae71bf43868961b25b11a125267f6d608a67a1ac",
  "Packaged": {
    "Date": "2026-10-10 11:12:47 UTC",
    "User": "root"
  },
  "Author": "Deepank Korandla [aut],\nNicholas Cooley [cre] (ORCID: <https://orcid.org/0000-0002-6029-304X>)",
  "Maintainer": "Nicholas Cooley <npc19@pitt.edu>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "AssessORFData_1.30.0.tar.gz",
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  "_expires": "2027-01-18T11:35:21.000Z",
  "_created": "2026-10-10T11:12:47.000Z",
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  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047362454",
  "_status": "success",
  "_host": "GitHub-Actions",
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    "warning": 0,
    "note": 8
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  "_commit": {
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    "author": "lshep <lori.shepherd@roswellpark.org>",
    "committer": "lshep <lori.shepherd@roswellpark.org>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379540
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  "_maintainer": {
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    "email": "npc19@pitt.edu",
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    {
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    },
    {
      "package": "AssessORF",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
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    "bacillus_subtilis_data",
    "escherichia_coli_data",
    "pseudomonas_aeruginosa_data",
    "staphylococcus_aureus_data",
    "genome",
    "proteome",
    "sequencingdata",
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    "extra/citation.html",
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    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
  ],
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    "GetStrainIDs",
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      "title": "'Assessment' Objects for _Streptococcus pyogenes_ strain AP1",
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    },
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      ],
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    },
    {
      "name": "AssessORF_StrainIDs",
      "title": "Vector of strain IDs used in the package",
      "object": "AssessORF_StrainIDs",
      "file": "AssessORF_StrainIDs.rda",
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      ],
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    {
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    },
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      "name": "ATCC11842_PreSaved_ResultsObj_Glimmer",
      "title": "'Assessment' Objects for _Lactobacillus delbrueckii_ subsp. _bulgaricus_ strain ATCC 11842",
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      "title": "'Assessment' Objects for _Pseudomonas pseudoalcaligenes_ strain CECT 5344",
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      "title": "'Assessment' Objects for _Lactobacillus delbrueckii_ subsp. _lactis_ strain LBCNRZ327_V11",
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    {
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    {
      "name": "COH1_PreSaved_ResultsObj_Glimmer",
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      "name": "COH1_PreSaved_ResultsObj_Prodigal",
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    {
      "name": "D_UW_3_CX_PreSaved_DataMapObj",
      "title": "'Assessment' Objects for _Chlamydia trachomatis_ strain D/UW-3/CX",
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    {
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    {
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      "title": "'Assessment' Objects for _Chlamydia trachomatis_ strain D/UW-3/CX",
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    {
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    {
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    {
      "name": "EGD_e_PreSaved_DataMapObj",
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    {
      "name": "EGD_e_PreSaved_ResultsObj_GenBank",
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      "title": "'Assessment' Objects for _Listeria monocytogenes_ strain EGD-e",
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    {
      "name": "EGD_e_PreSaved_ResultsObj_Glimmer",
      "title": "'Assessment' Objects for _Listeria monocytogenes_ strain EGD-e",
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      "name": "EGD_e_PreSaved_ResultsObj_Prodigal",
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    {
      "name": "H37Rv_PreSaved_DataMapObj",
      "title": "'Assessment' Objects for _Mycobacterium tuberculosis_ strain H37Rv",
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      "name": "H37Rv_PreSaved_ResultsObj_GenBank",
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    {
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    {
      "name": "HG001_PreSaved_DataMapObj",
      "title": "'Assessment' Objects for _Staphylococcus aureus_ subsp. _aureus_ strain HG001",
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    {
      "name": "HG001_PreSaved_ResultsObj_GenBank",
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      "name": "Houston_1_PreSaved_DataMapObj",
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      "name": "Houston_1_PreSaved_ResultsObj_Prodigal",
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    {
      "name": "Il1403_PreSaved_DataMapObj",
      "title": "'Assessment' Objects for _Lactococcus lactis_ subsp. _lactis_ strain Il1403",
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    {
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    {
      "name": "Il1403_PreSaved_ResultsObj_GeneMarkS2",
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    {
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    {
      "name": "Il1403_PreSaved_ResultsObj_Prodigal",
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    {
      "name": "K_12_MG1655_PreSaved_DataMapObj",
      "title": "'Assessment' Objects for _Escherichia coli_ strain K-12 substrain MG1655",
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    {
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      "object": "K_12_MG1655_PreSaved_ResultsObj_GenBank",
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    {
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      "title": "'Assessment' Objects for _Escherichia coli_ strain K-12 substrain MG1655",
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    {
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    {
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    {
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    {
      "name": "LAL14_1_PreSaved_ResultsObj_Glimmer",
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    {
      "name": "LAL14_1_PreSaved_ResultsObj_Prodigal",
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      "object": "LAL14_1_PreSaved_ResultsObj_Prodigal",
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    {
      "name": "MG1363_PreSaved_DataMapObj",
      "title": "'Assessment' Objects for _Lactococcus lactis_ subsp. _cremoris_ strain MG1363",
      "object": "MG1363_PreSaved_DataMapObj",
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    {
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      "page": "ATCC11842",
      "title": "'Assessment' Objects for _Lactobacillus delbrueckii_ subsp. _bulgaricus_ strain ATCC 11842",
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    {
      "page": "ATCC13032",
      "title": "'Assessment' Objects for _Corynebacterium glutamicum_ strain ATCC 13032",
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        "ATCC13032_PreSaved_ResultsObj_GenBank",
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    {
      "page": "ATCC17978",
      "title": "'Assessment' Objects for _Acinetobacter baumannii_ strain ATCC 17978",
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    {
      "page": "ATCC700084",
      "title": "'Assessment' Objects for _Mycobacterium smegmatis_ strain ATCC 700084",
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        "ATCC700084_PreSaved_ResultsObj_GenBank",
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    {
      "page": "BW25113",
      "title": "'Assessment' Objects for _Escherichia coli_ strain BW25113",
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    {
      "page": "CCMP1375",
      "title": "'Assessment' Objects for _Prochlorococcus marinus_ subsp. _marinus_ strain CCMP1375",
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    {
      "page": "CECT5344",
      "title": "'Assessment' Objects for _Pseudomonas pseudoalcaligenes_ strain CECT 5344",
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    },
    {
      "page": "CNRZ327",
      "title": "'Assessment' Objects for _Lactobacillus delbrueckii_ subsp. _lactis_ strain LBCNRZ327_V11",
      "topics": [
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    {
      "page": "COH1",
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    {
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    {
      "page": "EGD_e",
      "title": "'Assessment' Objects for _Listeria monocytogenes_ strain EGD-e",
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        "EGD_e_PreSaved_ResultsObj_Prodigal"
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    },
    {
      "page": "GetDataMapObj",
      "title": "Get a Data Map Object",
      "topics": [
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    },
    {
      "page": "GetGeneSources",
      "title": "Get the Gene Sources",
      "topics": [
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    },
    {
      "page": "GetResultsObj",
      "title": "Get a Results Object",
      "topics": [
        "GetResultsObj"
      ]
    },
    {
      "page": "GetStrainIDs",
      "title": "Get the Strain Identifiers",
      "topics": [
        "GetStrainIDs"
      ]
    },
    {
      "page": "H37Rv",
      "title": "'Assessment' Objects for _Mycobacterium tuberculosis_ strain H37Rv",
      "topics": [
        "H37Rv",
        "H37Rv_PreSaved_DataMapObj",
        "H37Rv_PreSaved_ResultsObj_GenBank",
        "H37Rv_PreSaved_ResultsObj_GeneMarkS2",
        "H37Rv_PreSaved_ResultsObj_Glimmer",
        "H37Rv_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "HG001",
      "title": "'Assessment' Objects for _Staphylococcus aureus_ subsp. _aureus_ strain HG001",
      "topics": [
        "HG001",
        "HG001_PreSaved_DataMapObj",
        "HG001_PreSaved_ResultsObj_GenBank",
        "HG001_PreSaved_ResultsObj_GeneMarkS2",
        "HG001_PreSaved_ResultsObj_Glimmer",
        "HG001_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "Houston_1",
      "title": "'Assessment' Objects for _Bartonella henselae_ strain Houston-1",
      "topics": [
        "Houston_1",
        "Houston_1_PreSaved_DataMapObj",
        "Houston_1_PreSaved_ResultsObj_GenBank",
        "Houston_1_PreSaved_ResultsObj_GeneMarkS2",
        "Houston_1_PreSaved_ResultsObj_Glimmer",
        "Houston_1_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "Il1403",
      "title": "'Assessment' Objects for _Lactococcus lactis_ subsp. _lactis_ strain Il1403",
      "topics": [
        "Il1403",
        "Il1403_PreSaved_DataMapObj",
        "Il1403_PreSaved_ResultsObj_GenBank",
        "Il1403_PreSaved_ResultsObj_GeneMarkS2",
        "Il1403_PreSaved_ResultsObj_Glimmer",
        "Il1403_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "K_12_MG1655",
      "title": "'Assessment' Objects for _Escherichia coli_ strain K-12 substrain MG1655",
      "topics": [
        "K_12_MG1655",
        "K_12_MG1655_PreSaved_DataMapObj",
        "K_12_MG1655_PreSaved_ResultsObj_GenBank",
        "K_12_MG1655_PreSaved_ResultsObj_GeneMarkS2",
        "K_12_MG1655_PreSaved_ResultsObj_Glimmer",
        "K_12_MG1655_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "LAL14_1",
      "title": "'Assessment' Objects for _Sulfolobus islandicus_ strain LAL14/1",
      "topics": [
        "LAL14_1",
        "LAL14_1_PreSaved_DataMapObj",
        "LAL14_1_PreSaved_ResultsObj_GenBank",
        "LAL14_1_PreSaved_ResultsObj_GeneMarkS2",
        "LAL14_1_PreSaved_ResultsObj_Glimmer",
        "LAL14_1_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "MG1363",
      "title": "'Assessment' Objects for _Lactococcus lactis_ subsp. _cremoris_ strain MG1363",
      "topics": [
        "MG1363",
        "MG1363_PreSaved_DataMapObj",
        "MG1363_PreSaved_ResultsObj_GenBank",
        "MG1363_PreSaved_ResultsObj_GeneMarkS2",
        "MG1363_PreSaved_ResultsObj_Glimmer",
        "MG1363_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "MGAS5005",
      "title": "'Assessment' Objects for _Streptococcus pyogenes_ strain MGAS5005",
      "topics": [
        "MGAS5005",
        "MGAS5005_PreSaved_DataMapObj",
        "MGAS5005_PreSaved_ResultsObj_GenBank",
        "MGAS5005_PreSaved_ResultsObj_GeneMarkS2",
        "MGAS5005_PreSaved_ResultsObj_Glimmer",
        "MGAS5005_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "NCIB_3610",
      "title": "'Assessment' Objects for _Bacillus subtilis_ subsp. _subtilis_ strain NCIB 3610",
      "topics": [
        "NCIB_3610",
        "NCIB_3610_PreSaved_DataMapObj",
        "NCIB_3610_PreSaved_ResultsObj_GenBank",
        "NCIB_3610_PreSaved_ResultsObj_GeneMarkS2",
        "NCIB_3610_PreSaved_ResultsObj_Glimmer",
        "NCIB_3610_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "PAO1",
      "title": "'Assessment' Objects for _Pseudomonas aeruginosa_ strain PAO1",
      "topics": [
        "PAO1",
        "PAO1_PreSaved_DataMapObj",
        "PAO1_PreSaved_ResultsObj_GenBank",
        "PAO1_PreSaved_ResultsObj_GeneMarkS2",
        "PAO1_PreSaved_ResultsObj_Glimmer",
        "PAO1_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "SaveGenomeToPath",
      "title": "Save a Strain's Genome to a Directory",
      "topics": [
        "SaveGenomeToPath"
      ]
    },
    {
      "page": "SL1344",
      "title": "'Assessment' Objects for _Salmonella enterica_ subsp. _enterica_ serovar Typhimurium strain SL1344",
      "topics": [
        "SL1344",
        "SL1344_PreSaved_DataMapObj",
        "SL1344_PreSaved_ResultsObj_GenBank",
        "SL1344_PreSaved_ResultsObj_GeneMarkS2",
        "SL1344_PreSaved_ResultsObj_Glimmer",
        "SL1344_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "Strain10403S",
      "title": "'Assessment' Objects for _Listeria monocytogenes_ strain 10403S",
      "topics": [
        "Strain10403S",
        "Strain10403S_PreSaved_DataMapObj",
        "Strain10403S_PreSaved_ResultsObj_GenBank",
        "Strain10403S_PreSaved_ResultsObj_GeneMarkS2",
        "Strain10403S_PreSaved_ResultsObj_Glimmer",
        "Strain10403S_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "Strain168",
      "title": "'Assessment' Objects for _Bacillus subtilis_ subsp. _subtilis_ strain 168",
      "topics": [
        "Strain168",
        "Strain168_PreSaved_DataMapObj",
        "Strain168_PreSaved_ResultsObj_GenBank",
        "Strain168_PreSaved_ResultsObj_GeneMarkS2",
        "Strain168_PreSaved_ResultsObj_Glimmer",
        "Strain168_PreSaved_ResultsObj_Prodigal"
      ]
    },
    {
      "page": "TCH1516",
      "title": "'Assessment' Objects for _Staphylococcus aureus_ subsp. _aureus_ strain USA300_TCH1516",
      "topics": [
        "TCH1516",
        "TCH1516_PreSaved_DataMapObj",
        "TCH1516_PreSaved_ResultsObj_GenBank",
        "TCH1516_PreSaved_ResultsObj_GeneMarkS2",
        "TCH1516_PreSaved_ResultsObj_Glimmer",
        "TCH1516_PreSaved_ResultsObj_Prodigal"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/AssessORFData/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "DBI",
    "DECIPHER",
    "fastmap",
    "generics",
    "glue",
    "IRanges",
    "lifecycle",
    "memoise",
    "pkgconfig",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "AssessORFDataGuide.Rmd",
      "filename": "AssessORFDataGuide.html",
      "title": "Quick Guide to AssessORFData",
      "author": "Deepank Korandla",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Strains and Gene Sources",
        "Getting the Objects",
        "Saving the Genome",
        "Session Info"
      ],
      "created": "2018-10-24 21:03:45",
      "modified": "2018-12-25 22:13:20",
      "commits": 4
    }
  ],
  "_score": 4,
  "_indexed": false,
  "_nocasepkg": "assessorfdata",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/AssessORFData",
  "_binaries": [
    {
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      "os": "linux",
      "version": "1.30.0",
      "date": "2026-10-10T11:31:23.000Z",
      "distro": "resolute",
      "commit": "ae71bf43868961b25b11a125267f6d608a67a1ac",
      "fileid": "https://r2.ropensci.org/0da405fd3815b1e686a23f23119d7ba5bbab5f88678aefd0076970238b5b6aab",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047362454"
    },
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      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047362454"
    }
  ]
}