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
gdb.create              Creates a new Genomic Database
gdb.get_readonly_attrs
                        Returns a list of read-only track attributes
gdb.reload              Reloads database from the disk
gdb.set_readonly_attrs
                        Sets read-only track attributes
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
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.all          Returns 1D intervals that cover the whole
                        genome
gintervals.canonic      Converts intervals to canonic form
gintervals.chrom_sizes
                        Returns number of intervals per chromosome
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.import_genes
                        Imports genes and annotations from files
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.neighbors    Finds neighbors between two sets of intervals
gintervals.quantiles    Calculates quantiles of a track expression for
                        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.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
gsample                 Returns samples from the values of track
                        expression
gscreen                 Finds intervals that match track expression
gsegment                Divides track expression into segments
gseq.extract            Returns DNA sequences
gsetroot                Initializes connection with Genomic Database
gsummary                Calculates summary statistics of track
                        expression
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.create           Creates a track from a track expression
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.exists           Tests for a track existence
gtrack.import           Creates a track from WIG / BigWig / BedGraph /
                        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.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.create          Creates a new 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
