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_dense()`	Creates a 'Dense' track from intervals and values
`gtrack.create_dirs()`	Create directories needed for track creation
`gtrack.dbs()`	Returns the database paths that contain track(s)
`gtrack.dataset()`	Returns the database/dataset path for a track
`gtrack.exists()`	Tests for a track existence
`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.path()`	Returns the path on disk of 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.copy()`	Copies 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
`gtrack.convert_to_indexed()`	Convert a track to indexed format
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
`gvtrack.filter()`	Attach or clear a genomic mask filter on 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.mark_overlaps()`	Mark overlapping intervals with a group ID
`gintervals.chrom_sizes()`	Returns number of intervals per chromosome
`gintervals.covered_bp()`	Calculate total base pairs covered by intervals
`gintervals.coverage_fraction()`	Calculate fraction of genomic space 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.normalize()`	Normalize intervals to fixed or variable sizes
`gintervals.annotate()`	Annotates 1D intervals using nearest neighbors
`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.as_chain()`	Transforms existing intervals to a chain format
`gintervals.path()`	Returns the path on disk of an interval set
`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.neighbors.upstream()` `gintervals.neighbors.downstream()` `gintervals.neighbors.directional()`	Directional neighbor finding functions
`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.union()`	Calculates a union of two sets of intervals
`gintervals.update()`	Updates a named intervals set
`gintervals.2d.convert_to_indexed()`	Convert 2D interval set to indexed format
`gintervals.convert_to_indexed()`	Convert 1D interval set to indexed format
`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
`gcor()`	Calculates correlation between track expressions
`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
`gsummary()`	Calculates summary statistics of track expression
Sequence functions Sequence functions
`gseq.extract()`	Returns DNA sequences
`gseq.pwm()`	Score DNA sequences with a PWM over a region of interest
`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.revcomp()`	Get reverse complement of DNA sequence
`grevcomp()`	Get reverse complement of DNA sequence
`gseq.rev()`	Reverse DNA sequence
`gseq.comp()`	Complement DNA sequence
Synthetic genome functions Generate synthetic genomes using stratified Markov models
`gsynth.train()`	Train a stratified Markov-5 model from genome sequences
`gsynth.sample()`	Sample a synthetic genome from a trained Markov model
`gsynth.random()`	Generate random genome sequences
`gsynth.replace_kmer()`	Iteratively replace a k-mer in the genome
`gsynth.save()`	Save a gsynth.model to disk
`gsynth.load()`	Load a gsynth.model from disk
`gsynth.bin_map()`	Create a bin mapping from value-based merge specifications
`print(<gsynth.model>)`	Print summary of a gsynth.model
Database functions Database functions
`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.get_readonly_attrs()`	Returns a list of read-only track attributes
`gdb.info()`	Get Database Information
`gdb.init()` `gdb.init_examples()` `gsetroot()`	Initializes connection with Genomic Database
`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.convert_to_indexed()`	Change Database to Indexed Genome Format
`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
Dataset functions Functions for managing datasets (multiple data sources)
`gdataset.load()`	Load a dataset into the namespace
`gdataset.unload()`	Unload a dataset from the namespace
`gdataset.save()`	Save a dataset
`gdataset.ls()`	List working database and loaded datasets
`gdataset.info()`	Get dataset information
`gdataset.example_path()`	Create an example dataset on the fly
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

Sequence functions

Synthetic genome functions

Database functions

Dataset functions

Other functions