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  "Type": "Package",
  "Package": "misha",
  "Title": "Toolkit for Analysis of Genomic Data",
  "Version": "5.10.3",
  "Authors@R": "c(\nperson(\"Misha\", \"Hoichman\", , \"misha@hoichman.com\", role = \"aut\"),\nperson(\"Aviezer\", \"Lifshitz\", , \"aviezer.lifshitz@weizmann.ac.il\", role = c(\"aut\", \"cre\")),\nperson(\"Eitan\", \"Yaffe\", , \"eitan.yaffe@weizmann.ac.il\", role = \"aut\"),\nperson(\"Amos\", \"Tanay\", , \"amos.tanay@weizmann.ac.il\", role = \"aut\"),\nperson(\"Weizmann Institute of Science\", role=\"cph\")\n)",
  "Description": "A toolkit for analysis of genomic data. The 'misha'\npackage implements an efficient data structure for storing\ngenomic data, and provides a set of functions for data\nextraction, manipulation and analysis. Some of the 2D genome\nalgorithms were described in Yaffe and Tanay (2011)\n<doi:10.1038/ng.947>.",
  "License": "MIT + file LICENSE",
  "URL": "https://tanaylab.github.io/misha/,\nhttps://github.com/tanaylab/misha",
  "BugReports": "https://github.com/tanaylab/misha/issues",
  "SystemRequirements": "samtools (>= 1.0; optional, required only for BAM\ninput)",
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  "Repository": "https://tanaylab.r-universe.dev",
  "Date/Publication": "2026-06-04 18:46:45 UTC",
  "RemoteUrl": "https://github.com/tanaylab/misha",
  "RemoteRef": "HEAD",
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  "Packaged": {
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    "User": "root"
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  "Author": "Misha Hoichman [aut],\nAviezer Lifshitz [aut, cre],\nEitan Yaffe [aut],\nAmos Tanay [aut],\nWeizmann Institute of Science [cph]",
  "Maintainer": "Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>",
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  "_created": "2026-06-04T19:27:35.000Z",
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    "message": "fix(C++): two perf-audit regressions - indexed empty-contig stale mmap + pwm below N-skip (5.10.3) (#135)\n\nIndexed dense tracks returned a prior chromosome's values for an empty (length-0) contig read after a populated one (stale mmap window, from 1cbfa801/v5.6.7). pwm.edit_distance direction=below with max_edits dropped N-heavy windows (direction-agnostic N-count skip, from cb1f287a/v5.6.11). Both fixed with regression tests confirmed red pre-fix, green after.",
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      "page": "misha-package",
      "title": "Toolkit for analysis of genomic data",
      "topics": [
        "misha-package",
        "misha"
      ]
    },
    {
      "page": "gbins.quantiles",
      "title": "Calculates quantiles of a track expression for bins",
      "topics": [
        "gbins.quantiles"
      ]
    },
    {
      "page": "gbins.summary",
      "title": "Calculates summary statistics of a track expression for bins",
      "topics": [
        "gbins.summary"
      ]
    },
    {
      "page": "gcis_decay",
      "title": "Calculates distribution of contact distances",
      "topics": [
        "gcis_decay"
      ]
    },
    {
      "page": "gcluster.run",
      "title": "Runs R commands on a cluster",
      "topics": [
        "gcluster.run"
      ]
    },
    {
      "page": "gcompute_strands_autocorr",
      "title": "Computes auto-correlation between the strands for a file of mapped sequences",
      "topics": [
        "gcompute_strands_autocorr"
      ]
    },
    {
      "page": "gcor",
      "title": "Calculates correlation between track expressions",
      "topics": [
        "gcor"
      ]
    },
    {
      "page": "gdataset.example_path",
      "title": "Create an example dataset on the fly",
      "topics": [
        "gdataset.example_path"
      ]
    },
    {
      "page": "gdataset.info",
      "title": "Get dataset information",
      "topics": [
        "gdataset.info"
      ]
    },
    {
      "page": "gdataset.load",
      "title": "Load a dataset into the namespace",
      "topics": [
        "gdataset.load"
      ]
    },
    {
      "page": "gdataset.ls",
      "title": "List working database and loaded datasets",
      "topics": [
        "gdataset.ls"
      ]
    },
    {
      "page": "gdataset.save",
      "title": "Save a dataset",
      "topics": [
        "gdataset.save"
      ]
    },
    {
      "page": "gdataset.unload",
      "title": "Unload a dataset from the namespace",
      "topics": [
        "gdataset.unload"
      ]
    },
    {
      "page": "gdb.build_genome",
      "title": "Build a misha genome database from a name",
      "topics": [
        "gdb.build_genome"
      ]
    },
    {
      "page": "gdb.convert_to_indexed",
      "title": "Change Database to Indexed Genome Format",
      "topics": [
        "gdb.convert_to_indexed"
      ]
    },
    {
      "page": "gdb.create",
      "title": "Creates a new Genomic Database",
      "topics": [
        "gdb.create"
      ]
    },
    {
      "page": "gdb.create_genome",
      "title": "Create and Load a Genome Database",
      "topics": [
        "gdb.create_genome"
      ]
    },
    {
      "page": "gdb.create_linked",
      "title": "Create a linked database with symlinks to a parent database",
      "topics": [
        "gdb.create_linked"
      ]
    },
    {
      "page": "gdb.export_fasta",
      "title": "Export a database genome as FASTA",
      "topics": [
        "gdb.export_fasta"
      ]
    },
    {
      "page": "gdb.genome_info",
      "title": "Inspect a resolved genome recipe without building",
      "topics": [
        "gdb.genome_info"
      ]
    },
    {
      "page": "gdb.get_readonly_attrs",
      "title": "Returns a list of read-only track attributes",
      "topics": [
        "gdb.get_readonly_attrs"
      ]
    },
    {
      "page": "gdb.info",
      "title": "Get Database Information",
      "topics": [
        "gdb.info"
      ]
    },
    {
      "page": "gdb.init",
      "title": "Initializes connection with Genomic Database",
      "topics": [
        "gdb.init",
        "gsetroot"
      ]
    },
    {
      "page": "gdb.init_examples",
      "title": "Initialise the example Genomic Database",
      "topics": [
        "gdb.init.examples",
        "gdb.init_examples"
      ]
    },
    {
      "page": "gdb.install_gff3_converter",
      "title": "Pre-install UCSC's gff3ToGenePred binary",
      "topics": [
        "gdb.install_gff3_converter"
      ]
    },
    {
      "page": "gdb.install_gtf_converter",
      "title": "Pre-install UCSC's gtfToGenePred binary",
      "topics": [
        "gdb.install_gtf_converter"
      ]
    },
    {
      "page": "gdb.install_intervals",
      "title": "Install interval sets onto an existing groot",
      "topics": [
        "gdb.install_intervals"
      ]
    },
    {
      "page": "gdb.list_genomes",
      "title": "List resolvable genome names",
      "topics": [
        "gdb.list_genomes"
      ]
    },
    {
      "page": "gdb.mark_cache_dirty",
      "title": "Mark cached track list as dirty",
      "topics": [
        "gdb.mark_cache_dirty"
      ]
    },
    {
      "page": "gdb.reload",
      "title": "Reloads database from the disk",
      "topics": [
        "gdb.reload"
      ]
    },
    {
      "page": "gdb.set_readonly_attrs",
      "title": "Sets read-only track attributes",
      "topics": [
        "gdb.set_readonly_attrs"
      ]
    },
    {
      "page": "gdb.unload",
      "title": "Unloads the genome database",
      "topics": [
        "gdb.unload"
      ]
    },
    {
      "page": "gdir.cd",
      "title": "Changes current working directory in Genomic Database",
      "topics": [
        "gdir.cd"
      ]
    },
    {
      "page": "gdir.create",
      "title": "Creates a new directory in Genomic Database",
      "topics": [
        "gdir.create"
      ]
    },
    {
      "page": "gdir.cwd",
      "title": "Returns the current working directory in Genomic Database",
      "topics": [
        "gdir.cwd"
      ]
    },
    {
      "page": "gdir.rm",
      "title": "Deletes a directory from Genomic Database",
      "topics": [
        "gdir.rm"
      ]
    },
    {
      "page": "gdist",
      "title": "Calculates distribution of track expressions",
      "topics": [
        "gdist"
      ]
    },
    {
      "page": "gextract",
      "title": "Returns evaluated track expression",
      "topics": [
        "gextract"
      ]
    },
    {
      "page": "ggenome.implant",
      "title": "Implant donor sequences into a reference genome",
      "topics": [
        "ggenome.implant"
      ]
    },
    {
      "page": "ggenome.transplant",
      "title": "Transplant sequences from one genome into another",
      "topics": [
        "ggenome.transplant"
      ]
    },
    {
      "page": "gintervals",
      "title": "Creates a set of 1D intervals",
      "topics": [
        "gintervals"
      ]
    },
    {
      "page": "gintervals.2d",
      "title": "Creates a set of 2D intervals",
      "topics": [
        "gintervals.2d"
      ]
    },
    {
      "page": "gintervals.2d.all",
      "title": "Returns 2D intervals that cover the whole genome",
      "topics": [
        "gintervals.2d.all"
      ]
    },
    {
      "page": "gintervals.2d.band_intersect",
      "title": "Intersects two-dimensional intervals with a band",
      "topics": [
        "gintervals.2d.band_intersect"
      ]
    },
    {
      "page": "gintervals.2d.convert_to_indexed",
      "title": "Convert 2D interval set to indexed format",
      "topics": [
        "gintervals.2d.convert_to_indexed"
      ]
    },
    {
      "page": "gintervals.2d.intersect",
      "title": "Intersects two sets of 2D intervals",
      "topics": [
        "gintervals.2d.intersect"
      ]
    },
    {
      "page": "gintervals.2d.union",
      "title": "Unites two sets of 2D intervals",
      "topics": [
        "gintervals.2d.union"
      ]
    },
    {
      "page": "gintervals.all",
      "title": "Returns 1D intervals that cover the whole genome",
      "topics": [
        "gintervals.all"
      ]
    },
    {
      "page": "gintervals.annotate",
      "title": "Annotates 1D intervals using nearest neighbors",
      "topics": [
        "gintervals.annotate"
      ]
    },
    {
      "page": "gintervals.as_chain",
      "title": "Transforms existing intervals to a chain format",
      "topics": [
        "gintervals.as_chain"
      ]
    },
    {
      "page": "gintervals.attr.export",
      "title": "Returns interval set attributes values",
      "topics": [
        "gintervals.attr.export"
      ]
    },
    {
      "page": "gintervals.attr.get",
      "title": "Returns value of an interval set attribute",
      "topics": [
        "gintervals.attr.get"
      ]
    },
    {
      "page": "gintervals.attr.import",
      "title": "Imports interval set attributes values",
      "topics": [
        "gintervals.attr.import"
      ]
    },
    {
      "page": "gintervals.attr.set",
      "title": "Assigns value to an interval set attribute",
      "topics": [
        "gintervals.attr.set"
      ]
    },
    {
      "page": "gintervals.canonic",
      "title": "Converts intervals to canonic form",
      "topics": [
        "gintervals.canonic"
      ]
    },
    {
      "page": "gintervals.chrom_sizes",
      "title": "Returns number of intervals per chromosome",
      "topics": [
        "gintervals.chrom_sizes"
      ]
    },
    {
      "page": "gintervals.convert_to_indexed",
      "title": "Convert 1D interval set to indexed format",
      "topics": [
        "gintervals.convert_to_indexed"
      ]
    },
    {
      "page": "gintervals.coverage_fraction",
      "title": "Calculate fraction of genomic space covered by intervals",
      "topics": [
        "gintervals.coverage_fraction"
      ]
    },
    {
      "page": "gintervals.covered_bp",
      "title": "Calculate total base pairs covered by intervals",
      "topics": [
        "gintervals.covered_bp"
      ]
    },
    {
      "page": "gintervals.dataset",
      "title": "Returns the database/dataset path for interval sets",
      "topics": [
        "gintervals.dataset"
      ]
    },
    {
      "page": "gintervals.dbs",
      "title": "Returns all database paths containing an interval set",
      "topics": [
        "gintervals.dbs"
      ]
    },
    {
      "page": "gintervals.diff",
      "title": "Calculates difference of two intervals sets",
      "topics": [
        "gintervals.diff"
      ]
    },
    {
      "page": "gintervals.exists",
      "title": "Tests for a named intervals set existence",
      "topics": [
        "gintervals.exists"
      ]
    },
    {
      "page": "gintervals.force_range",
      "title": "Limits intervals to chromosomal range",
      "topics": [
        "gintervals.force_range"
      ]
    },
    {
      "page": "gintervals.from_mat",
      "title": "Convert an interval-indexed matrix back to an intervals + values data.frame",
      "topics": [
        "gintervals.from_mat"
      ]
    },
    {
      "page": "gintervals.from_strings",
      "title": "Creates 1D intervals from coordinate strings",
      "topics": [
        "gintervals.from_strings"
      ]
    },
    {
      "page": "gintervals.import_bed",
      "title": "Import intervals from a BED file",
      "topics": [
        "gintervals.import_bed"
      ]
    },
    {
      "page": "gintervals.import_genes",
      "title": "Imports genes and annotations from files",
      "topics": [
        "gintervals.import_genes"
      ]
    },
    {
      "page": "gintervals.import_gff",
      "title": "Import intervals from a GFF/GTF file",
      "topics": [
        "gintervals.import_gff"
      ]
    },
    {
      "page": "gintervals.import_vcf",
      "title": "Import intervals from a VCF file",
      "topics": [
        "gintervals.import_vcf"
      ]
    },
    {
      "page": "gintervals.intersect",
      "title": "Calculates an intersection of two sets of intervals",
      "topics": [
        "gintervals.intersect"
      ]
    },
    {
      "page": "gintervals.is.bigset",
      "title": "Tests for big intervals set",
      "topics": [
        "gintervals.is.bigset"
      ]
    },
    {
      "page": "gintervals.liftover",
      "title": "Converts intervals from another assembly",
      "topics": [
        "gintervals.liftover"
      ]
    },
    {
      "page": "gintervals.load",
      "title": "Loads a named intervals set",
      "topics": [
        "gintervals.load"
      ]
    },
    {
      "page": "gintervals.load_chain",
      "title": "Loads assembly conversion table from a chain file",
      "topics": [
        "gintervals.load_chain"
      ]
    },
    {
      "page": "gintervals.ls",
      "title": "Returns a list of named intervals sets",
      "topics": [
        "gintervals.ls"
      ]
    },
    {
      "page": "gintervals.mapply",
      "title": "Applies a function to values of track expressions",
      "topics": [
        "gintervals.mapply"
      ]
    },
    {
      "page": "gintervals.mark_overlaps",
      "title": "Mark overlapping intervals with a group ID",
      "topics": [
        "gintervals.mark_overlaps"
      ]
    },
    {
      "page": "gintervals.neighbors",
      "title": "Finds neighbors between two sets of intervals",
      "topics": [
        "gintervals.neighbors"
      ]
    },
    {
      "page": "directional-neighbors",
      "title": "Directional neighbor finding functions",
      "topics": [
        "gintervals.neighbors.directional",
        "gintervals.neighbors.downstream",
        "gintervals.neighbors.upstream"
      ]
    },
    {
      "page": "gintervals.normalize",
      "title": "Normalize intervals to fixed or variable sizes",
      "topics": [
        "gintervals.normalize"
      ]
    },
    {
      "page": "gintervals.path",
      "title": "Returns the path on disk of an interval set",
      "topics": [
        "gintervals.path"
      ]
    },
    {
      "page": "gintervals.quantiles",
      "title": "Calculates quantiles of a track expression for intervals",
      "topics": [
        "gintervals.quantiles"
      ]
    },
    {
      "page": "gintervals.random",
      "title": "Generate random genome intervals",
      "topics": [
        "gintervals.random"
      ]
    },
    {
      "page": "gintervals.rbind",
      "title": "Combines several sets of intervals",
      "topics": [
        "gintervals.rbind"
      ]
    },
    {
      "page": "gintervals.rm",
      "title": "Deletes a named intervals set",
      "topics": [
        "gintervals.rm"
      ]
    },
    {
      "page": "gintervals.save",
      "title": "Creates a named intervals set",
      "topics": [
        "gintervals.save"
      ]
    },
    {
      "page": "gintervals.summary",
      "title": "Calculates summary statistics of track expression for intervals",
      "topics": [
        "gintervals.summary"
      ]
    },
    {
      "page": "gintervals.to_mat",
      "title": "Convert intervals + values data.frame to an interval-indexed matrix",
      "topics": [
        "gintervals.to_mat"
      ]
    },
    {
      "page": "gintervals.union",
      "title": "Calculates a union of two sets of intervals",
      "topics": [
        "gintervals.union"
      ]
    },
    {
      "page": "gintervals.update",
      "title": "Updates a named intervals set",
      "topics": [
        "gintervals.update"
      ]
    },
    {
      "page": "giterator.cartesian_grid",
      "title": "Creates a cartesian-grid iterator",
      "topics": [
        "giterator.cartesian_grid"
      ]
    },
    {
      "page": "giterator.intervals",
      "title": "Returns iterator intervals",
      "topics": [
        "giterator.intervals"
      ]
    },
    {
      "page": "glookup",
      "title": "Returns values from a lookup table based on track expression",
      "topics": [
        "glookup"
      ]
    },
    {
      "page": "gpartition",
      "title": "Partitions the values of track expression",
      "topics": [
        "gpartition"
      ]
    },
    {
      "page": "gquantiles",
      "title": "Calculates quantiles of a track expression",
      "topics": [
        "gquantiles"
      ]
    },
    {
      "page": "grevcomp",
      "title": "Get reverse complement of DNA sequence",
      "topics": [
        "grevcomp"
      ]
    },
    {
      "page": "gsample",
      "title": "Returns samples from the values of track expression",
      "topics": [
        "gsample"
      ]
    },
    {
      "page": "gscreen",
      "title": "Finds intervals that match track expression",
      "topics": [
        "gscreen"
      ]
    },
    {
      "page": "gsegment",
      "title": "Divides track expression into segments",
      "topics": [
        "gsegment"
      ]
    },
    {
      "page": "gseq.comp",
      "title": "Complement DNA sequence",
      "topics": [
        "gseq.comp"
      ]
    },
    {
      "page": "gseq.extract",
      "title": "Returns DNA sequences",
      "topics": [
        "gseq.extract"
      ]
    },
    {
      "page": "gseq.kmer",
      "title": "Score DNA sequences with a k-mer over a region of interest",
      "topics": [
        "gseq.kmer"
      ]
    },
    {
      "page": "gseq.kmer.dist",
      "title": "Compute k-mer distribution in genomic intervals",
      "topics": [
        "gseq.kmer.dist"
      ]
    },
    {
      "page": "gseq.pwm",
      "title": "Score DNA sequences with a PWM over a region of interest",
      "topics": [
        "gseq.pwm"
      ]
    },
    {
      "page": "gseq.pwm_edits",
      "title": "Show optimal edits to reach a PWM score threshold",
      "topics": [
        "gseq.pwm_edits"
      ]
    },
    {
      "page": "gseq.read_homer",
      "title": "Read motifs from a HOMER motif format file",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "gseq.read_homer"
      ]
    },
    {
      "page": "gseq.read_jaspar",
      "title": "Read motifs from a JASPAR PFM format file",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "gseq.read_jaspar"
      ]
    },
    {
      "page": "gseq.read_meme",
      "title": "Read motifs from a MEME minimal motif format file",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "gseq.read_meme"
      ]
    },
    {
      "page": "gseq.rev",
      "title": "Reverse DNA sequence",
      "topics": [
        "gseq.rev"
      ]
    },
    {
      "page": "gseq.revcomp",
      "title": "Get reverse complement of DNA sequence",
      "topics": [
        "gseq.revcomp"
      ]
    },
    {
      "page": "gsummary",
      "title": "Calculates summary statistics of track expression",
      "topics": [
        "gsummary"
      ]
    },
    {
      "page": "gsynth.bin_map",
      "title": "Create a bin mapping from value-based merge specifications",
      "topics": [
        "gsynth.bin_map"
      ]
    },
    {
      "page": "gsynth.cell_merge",
      "title": "Resolve a cell-level merge specification into flat bin indices",
      "topics": [
        "gsynth.cell_merge"
      ]
    },
    {
      "page": "gsynth.convert",
      "title": "Convert a legacy RDS gsynth model to .gsm format",
      "topics": [
        "gsynth.convert"
      ]
    },
    {
      "page": "gsynth.forbid_kmer",
      "title": "Forbid a k-mer pattern in a trained gsynth model",
      "topics": [
        "gsynth.forbid_kmer"
      ]
    },
    {
      "page": "gsynth.load",
      "title": "Load a gsynth.model from disk",
      "topics": [
        "gsynth.load"
      ]
    },
    {
      "page": "gsynth.random",
      "title": "Generate random genome sequences",
      "topics": [
        "gsynth.random"
      ]
    },
    {
      "page": "gsynth.replace_kmer",
      "title": "Iteratively replace a k-mer in the genome",
      "topics": [
        "gsynth.replace_kmer"
      ]
    },
    {
      "page": "gsynth.sample",
      "title": "Sample a synthetic genome from a trained Markov model",
      "topics": [
        "gsynth.sample"
      ]
    },
    {
      "page": "gsynth.save",
      "title": "Save a gsynth.model to disk in .gsm format",
      "topics": [
        "gsynth.save"
      ]
    },
    {
      "page": "gsynth.score",
      "title": "Score the genome under a trained gsynth model",
      "topics": [
        "gsynth.score"
      ]
    },
    {
      "page": "gsynth.train",
      "title": "Train a stratified Markov model from genome sequences",
      "topics": [
        "gsynth.train"
      ]
    },
    {
      "page": "gtrack.2d.convert_to_indexed",
      "title": "Convert 2D track to indexed format",
      "topics": [
        "gtrack.2d.convert_to_indexed"
      ]
    },
    {
      "page": "gtrack.2d.create",
      "title": "Creates a 'Rectangles' track from intervals and values",
      "topics": [
        "gtrack.2d.create"
      ]
    },
    {
      "page": "gtrack.2d.import",
      "title": "Creates a 2D track from tab-delimited file",
      "topics": [
        "gtrack.2d.import"
      ]
    },
    {
      "page": "gtrack.2d.import_contacts",
      "title": "Creates a track from a file of inter-genomic contacts",
      "topics": [
        "gtrack.2d.import_contacts"
      ]
    },
    {
      "page": "gtrack.array.extract",
      "title": "Returns values from 'Array' track",
      "topics": [
        "gtrack.array.extract"
      ]
    },
    {
      "page": "gtrack.array.get_colnames",
      "title": "Returns column names of array track",
      "topics": [
        "gtrack.array.get_colnames"
      ]
    },
    {
      "page": "gtrack.array.import",
      "title": "Creates an array track from array tracks or files",
      "topics": [
        "gtrack.array.import"
      ]
    },
    {
      "page": "gtrack.array.set_colnames",
      "title": "Sets column names of array track",
      "topics": [
        "gtrack.array.set_colnames"
      ]
    },
    {
      "page": "gtrack.attr.export",
      "title": "Returns track attributes values",
      "topics": [
        "gtrack.attr.export"
      ]
    },
    {
      "page": "gtrack.attr.get",
      "title": "Returns value of a track attribute",
      "topics": [
        "gtrack.attr.get"
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    {
      "page": "gtrack.attr.import",
      "title": "Imports track attributes values",
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    {
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      "topics": [
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