Package index • misha

Track functions Functions to manipulate and create tracks
`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_pwm_energy()`	Creates a new track from PSSM energy function
`gtrack.create_sparse()`	Creates a 'Sparse' track from intervals and values
`gtrack.create_dirs()`	Create directories needed for track creation
`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
Virtual track functions Functions to manipulate and create virtual tracks
`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
Intervals functions Functions to manipulate and create intervals
`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
Data manipulation functions Data manipulation functions
`gdist()`	Calculates distribution of track expressions
`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
`gcompute_strands_autocorr()`	Computes auto-correlation between the strands for a file of mapped sequences
`gextract()`	Returns evaluated track expression
`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
`gsummary()`	Calculates summary statistics of track expression
Database functions Database functions
`gdb.create_genome()`	Create and Load a Genome Database
`gdb.create()`	Creates a new Genomic Database
`gdb.get_readonly_attrs()`	Returns a list of read-only track attributes
`gsetroot()` `gdb.init()` `gdb.init_examples()`	Initializes connection with Genomic Database
`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
Other functions Other
`misha-package` `misha`	Toolkit for analysis of genomic data
`gcluster.run()`	Runs R commands on a cluster
`gwget()`	Downloads files from FTP server
`gwilcox()`	Calculates Wilcoxon test on sliding windows over track expression

Reference

Track functions

Virtual track functions

Intervals functions

Data manipulation functions

Database functions

Other functions