# Toolkit for Analysis of Genomic Data

## Documentation for package ‘misha’ version 4.3.11

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

misha-package | Toolkit for analysis of genomic data
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.create_genome | Create and Load a Genome Database
gdb.get_readonly_attrs | Returns a list of read-only track attributes
gdb.init | Initializes connection with Genomic Database
gdb.init.examples | Initializes connection with Genomic Database
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
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
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.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_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.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.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 | Toolkit for analysis of genomic data