{
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  "Package": "SingleMoleculeGenomicsIO",
  "Title": "Tools for reading single molecule genomics data",
  "Version": "0.1.9",
  "Authors@R": "c(\nperson(\"Michael\", \"Stadler\", , \"michael.stadler@fmi.ch\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-2269-4934\")),\nperson(\"Charlotte\", \"Soneson\", , \"charlotte.soneson@fmi.ch\",\nrole = \"aut\", comment = c(ORCID = \"0000-0003-3833-2169\")),\nperson(\"Panagiotis\", \"Papasaikas\", , \"panagiotis.papasaikas@fmi.ch\",\nrole = \"aut\", comment = c(ORCID = \"0000-0002-1640-7636\")),\nperson(\"Sebastien\", \"Smallwood\", , \"sebastien.smallwood@fmi.ch\",\nrole = \"aut\", comment = c(ORCID = \"0009-0006-8466-2459\")),\nperson(\"Friedrich Miescher Institute for Biomedical Research\", role = \"cph\")\n)",
  "Description": "Provides tools for reading of single-molecule genomics\ndata from different file formats in R. The package includes\nfunctions for reading collapsed or read-level data from modBAM,\nbedMethyl and `modkit extract` tabular files, as well as C-to-T\nconversion based BAM files, as `SummarizedExperiment` objects.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/fmicompbio/SingleMoleculeGenomicsIO,\nhttps://fmicompbio.github.io/SingleMoleculeGenomicsIO",
  "BugReports": "https://github.com/fmicompbio/SingleMoleculeGenomicsIO/issues",
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  "biocViews": "Epigenetics, LongRead",
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  "Repository": "https://fmicompbio.r-universe.dev",
  "Date/Publication": "2026-10-19 07:51:20 UTC",
  "RemoteUrl": "https://github.com/fmicompbio/SingleMoleculeGenomicsIO",
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  "Author": "Michael Stadler [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-2269-4934>),\nCharlotte Soneson [aut] (ORCID:\n<https://orcid.org/0000-0003-3833-2169>),\nPanagiotis Papasaikas [aut] (ORCID:\n<https://orcid.org/0000-0002-1640-7636>),\nSebastien Smallwood [aut] (ORCID:\n<https://orcid.org/0009-0006-8466-2459>),\nFriedrich Miescher Institute for Biomedical Research [cph]",
  "Maintainer": "Michael Stadler <michael.stadler@fmi.ch>",
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  "_published": "2026-10-26T11:04:50.972Z",
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      "title": "Count alignments in an indexed bam file",
      "topics": [
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    },
    {
      "page": "countMismatchStatePairs",
      "title": "Count pairs of modified bases by distance and modification state for bam files where modifications are indicated by sequence mismatches",
      "topics": [
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    },
    {
      "page": "countStatePairs",
      "title": "Count pairs of modified bases by distance and modification state",
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      "title": "Estimation of noise variance for time series.",
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      "title": "Expand the rows of a 'RangedSummarizedExperiment' to single base resolution.",
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      "page": "getReadLevelColDataNames",
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