gbins.quantiles         Calculates quantiles of a track expression for
                        bins
gbins.summary           Calculates summary statistics of a track
                        expression for bins
gcis_decay              Calculates distribution of contact distances
gcluster.run            Runs R commands on a cluster
gcompute_strands_autocorr
                        Computes auto-correlation between the strands
                        for a file of mapped sequences
gcor                    Calculates correlation between track
                        expressions
gdataset.example_path   Create an example dataset on the fly
gdataset.info           Get dataset information
gdataset.load           Load a dataset into the namespace
gdataset.ls             List working database and loaded datasets
gdataset.save           Save a dataset
gdataset.unload         Unload a dataset from the namespace
gdb.build_genome        Build a misha genome database from a name
gdb.convert_to_indexed
                        Change Database to Indexed Genome Format
gdb.create              Creates a new Genomic Database
gdb.create_genome       Create and Load a Genome Database
gdb.create_linked       Create a linked database with symlinks to a
                        parent database
gdb.export_fasta        Export a database genome as FASTA
gdb.genome_info         Inspect a resolved genome recipe without
                        building
gdb.get_readonly_attrs
                        Returns a list of read-only track attributes
gdb.info                Get Database Information
gdb.init                Initializes connection with Genomic Database
gdb.init_examples       Initialise the example Genomic Database
gdb.install_gff3_converter
                        Pre-install UCSC's gff3ToGenePred binary
gdb.install_gtf_converter
                        Pre-install UCSC's gtfToGenePred binary
gdb.install_intervals   Install interval sets onto an existing groot
gdb.list_genomes        List resolvable genome names
gdb.mark_cache_dirty    Mark cached track list as dirty
gdb.reload              Reloads database from the disk
gdb.set_readonly_attrs
                        Sets read-only track attributes
gdb.unload              Unloads the genome database
gdir.cd                 Changes current working directory in Genomic
                        Database
gdir.create             Creates a new directory in Genomic Database
gdir.cwd                Returns the current working directory in
                        Genomic Database
gdir.rm                 Deletes a directory from Genomic Database
gdist                   Calculates distribution of track expressions
gextract                Returns evaluated track expression
ggenome.implant         Implant donor sequences into a reference genome
ggenome.transplant      Transplant sequences from one genome into
                        another
gintervals              Creates a set of 1D intervals
gintervals.2d           Creates a set of 2D intervals
gintervals.2d.all       Returns 2D intervals that cover the whole
                        genome
gintervals.2d.band_intersect
                        Intersects two-dimensional intervals with a
                        band
gintervals.2d.convert_to_indexed
                        Convert 2D interval set to indexed format
gintervals.2d.intersect
                        Intersects two sets of 2D intervals
gintervals.2d.union     Unites two sets of 2D intervals
gintervals.all          Returns 1D intervals that cover the whole
                        genome
gintervals.annotate     Annotates 1D intervals using nearest neighbors
gintervals.as_chain     Transforms existing intervals to a chain format
gintervals.attr.export
                        Returns interval set attributes values
gintervals.attr.get     Returns value of an interval set attribute
gintervals.attr.import
                        Imports interval set attributes values
gintervals.attr.set     Assigns value to an interval set attribute
gintervals.canonic      Converts intervals to canonic form
gintervals.chrom_sizes
                        Returns number of intervals per chromosome
gintervals.convert_to_indexed
                        Convert 1D interval set to indexed format
gintervals.coverage_fraction
                        Calculate fraction of genomic space covered by
                        intervals
gintervals.covered_bp   Calculate total base pairs covered by intervals
gintervals.dataset      Returns the database/dataset path for interval
                        sets
gintervals.dbs          Returns all database paths containing an
                        interval set
gintervals.diff         Calculates difference of two intervals sets
gintervals.exists       Tests for a named intervals set existence
gintervals.force_range
                        Limits intervals to chromosomal range
gintervals.from_mat     Convert an interval-indexed matrix back to an
                        intervals + values data.frame
gintervals.from_strings
                        Creates 1D intervals from coordinate strings
gintervals.import_bed   Import intervals from a BED file
gintervals.import_genes
                        Imports genes and annotations from files
gintervals.import_gff   Import intervals from a GFF/GTF file
gintervals.import_vcf   Import intervals from a VCF file
gintervals.intersect    Calculates an intersection of two sets of
                        intervals
gintervals.is.bigset    Tests for big intervals set
gintervals.liftover     Converts intervals from another assembly
gintervals.load         Loads a named intervals set
gintervals.load_chain   Loads assembly conversion table from a chain
                        file
gintervals.ls           Returns a list of named intervals sets
gintervals.mapply       Applies a function to values of track
                        expressions
gintervals.mark_overlaps
                        Mark overlapping intervals with a group ID
gintervals.neighbors    Finds neighbors between two sets of intervals
gintervals.neighbors.upstream
                        Directional neighbor finding functions
gintervals.normalize    Normalize intervals to fixed or variable sizes
gintervals.path         Returns the path on disk of an interval set
gintervals.quantiles    Calculates quantiles of a track expression for
                        intervals
gintervals.random       Generate random genome intervals
gintervals.rbind        Combines several sets of intervals
gintervals.rm           Deletes a named intervals set
gintervals.save         Creates a named intervals set
gintervals.summary      Calculates summary statistics of track
                        expression for intervals
gintervals.to_mat       Convert intervals + values data.frame to an
                        interval-indexed matrix
gintervals.union        Calculates a union of two sets of intervals
gintervals.update       Updates a named intervals set
giterator.cartesian_grid
                        Creates a cartesian-grid iterator
giterator.intervals     Returns iterator intervals
glookup                 Returns values from a lookup table based on
                        track expression
gpartition              Partitions the values of track expression
gquantiles              Calculates quantiles of a track expression
grevcomp                Get reverse complement of DNA sequence
gsample                 Returns samples from the values of track
                        expression
gscreen                 Finds intervals that match track expression
gsegment                Divides track expression into segments
gseq.comp               Complement DNA sequence
gseq.extract            Returns DNA sequences
gseq.kmer               Score DNA sequences with a k-mer over a region
                        of interest
gseq.kmer.dist          Compute k-mer distribution in genomic intervals
gseq.pwm                Score DNA sequences with a PWM over a region of
                        interest
gseq.pwm_edits          Show optimal edits to reach a PWM score
                        threshold
gseq.read_homer         Read motifs from a HOMER motif format file
gseq.read_jaspar        Read motifs from a JASPAR PFM format file
gseq.read_meme          Read motifs from a MEME minimal motif format
                        file
gseq.rev                Reverse DNA sequence
gseq.revcomp            Get reverse complement of DNA sequence
gsummary                Calculates summary statistics of track
                        expression
gsynth.bin_map          Create a bin mapping from value-based merge
                        specifications
gsynth.cell_merge       Resolve a cell-level merge specification into
                        flat bin indices
gsynth.convert          Convert a legacy RDS gsynth model to .gsm
                        format
gsynth.forbid_kmer      Forbid a k-mer pattern in a trained gsynth
                        model
gsynth.load             Load a gsynth.model from disk
gsynth.random           Generate random genome sequences
gsynth.replace_kmer     Iteratively replace a k-mer in the genome
gsynth.sample           Sample a synthetic genome from a trained Markov
                        model
gsynth.save             Save a gsynth.model to disk in .gsm format
gsynth.score            Score the genome under a trained gsynth model
gsynth.train            Train a stratified Markov model from genome
                        sequences
gtrack.2d.convert_to_indexed
                        Convert 2D track to indexed format
gtrack.2d.create        Creates a 'Rectangles' track from intervals and
                        values
gtrack.2d.import        Creates a 2D track from tab-delimited file
gtrack.2d.import_contacts
                        Creates a track from a file of inter-genomic
                        contacts
gtrack.array.extract    Returns values from 'Array' track
gtrack.array.get_colnames
                        Returns column names of array track
gtrack.array.import     Creates an array track from array tracks or
                        files
gtrack.array.set_colnames
                        Sets column names of array track
gtrack.attr.export      Returns track attributes values
gtrack.attr.get         Returns value of a track attribute
gtrack.attr.import      Imports track attributes values
gtrack.attr.set         Assigns value to a track attribute
gtrack.convert          Converts a track to the most current format
gtrack.convert_to_indexed
                        Convert a track to indexed format
gtrack.copy             Copies one or more tracks
gtrack.create           Creates a track from a track expression
gtrack.create_dense     Creates a 'Dense' track from intervals and
                        values
gtrack.create_dirs      Create directories needed for track creation
gtrack.create_pwm_energy
                        Creates a new track from PSSM energy function
gtrack.create_sparse    Creates a 'Sparse' track from intervals and
                        values
gtrack.dataset          Returns the database/dataset path for a track
gtrack.dbs              Returns the database paths that contain
                        track(s)
gtrack.exists           Tests for a track existence
gtrack.export_bedgraph
                        Export a track to bedGraph format
gtrack.export_bigwig    Export a track to BigWig format
gtrack.import           Creates a track from WIG / BigWig / BedGraph /
                        BED / tab-delimited file
gtrack.import_mappedseq
                        Creates a track from a file of mapped sequences
gtrack.import_set       Creates one or more tracks from multiple WIG /
                        BigWig / BedGraph / tab-delimited files on disk
                        or FTP
gtrack.info             Returns information about a track
gtrack.liftover         Imports a track from another assembly
gtrack.lookup           Creates a new track from a lookup table based
                        on track expression
gtrack.ls               Returns a list of track names
gtrack.modify           Modifies track contents
gtrack.mv               Renames or moves a track
gtrack.path             Returns the path on disk of a track
gtrack.rm               Deletes a track
gtrack.smooth           Creates a new track from smoothed values of
                        track expression
gtrack.var.get          Returns value of a track variable
gtrack.var.ls           Returns a list of track variables for a track
gtrack.var.rm           Deletes a track variable
gtrack.var.set          Assigns value to a track variable
gvtrack.array.slice     Defines rules for a single value calculation of
                        a virtual 'Array' track
gvtrack.clear           Deletes all virtual tracks
gvtrack.create          Creates a new virtual track
gvtrack.filter          Attach or clear a genomic mask filter on a
                        virtual track
gvtrack.info            Returns the definition of a virtual track
gvtrack.iterator        Defines modification rules for a
                        one-dimensional iterator in a virtual track
gvtrack.iterator.2d     Defines modification rules for a
                        two-dimensional iterator in a virtual track
gvtrack.ls              Returns a list of virtual track names
gvtrack.rm              Deletes a virtual track
gwget                   Downloads files from FTP server
gwilcox                 Calculates Wilcoxon test on sliding windows
                        over track expression
misha-package           Toolkit for analysis of genomic data
print.gsynth.model      Print summary of a gsynth.model
