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misha

The misha package is a toolkit for analysis of genomic data. it implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis.

Installation

You can install the released version of misha from CRAN with:

install.packages("misha")

And the development version from GitHub with:

remotes::install_github("tanaylab/misha")

Usage

See the Genomes vignette for instructions on how to create a misha database for common genomes.

See the user manual for more usage details.

Running scripts from old versions of misha (< 4.2.0)

Starting in misha 4.2.0, the package no longer stores global variables such as ALLGENOME or GROOT. Instead, these variables are stored in a special environment called .misha. This means that scripts written for older versions of misha will no longer work. To run such scripts, either add a prefix of .misha$ to all those variables (.misha$ALLGENOME instead of ALLGENOME), or run the following command before running the script:

ALLGENOME <<- .misha$ALLGENOME
GROOT <<- .misha$GROOT
ALLGENOME <<- .misha$ALLGENOME
GINTERVID <<- .misha$GINTERVID
GITERATOR.INTERVALS <<- .misha$GITERATOR.INTERVALS
GROOT <<- .misha$GROOT
GWD <<- .misha$GWD
GTRACKS <<- .misha$GTRACKS

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Version

Install

install.packages('misha')

Monthly Downloads

106

Version

5.3.2

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/tanaylab/misha

Homepage

https://tanaylab.github.io/misha/

Maintainer

Aviezer Lifshitz

Last Published

December 14th, 2025

Functions in misha (5.3.2)

Get Database Information

Creates a set of 2D intervals

gintervals.annotate

Annotates 1D intervals using nearest neighbors

gintervals.as_chain

Transforms existing intervals to a chain format

Creates a set of 1D intervals

Returns 1D intervals that cover the whole genome

gintervals.convert_to_indexed

Convert 1D interval set to indexed format

gintervals.coverage_fraction

Calculate fraction of genomic space covered by intervals

gintervals.2d.convert_to_indexed

Convert 2D interval set to indexed format

gintervals.chrom_sizes

Returns number of intervals per chromosome

gintervals.2d.band_intersect

Intersects two-dimensional intervals with a band

gintervals.canonic

Converts intervals to canonic form

Returns evaluated track expression

Calculates distribution of track expressions

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.mark_overlaps

Mark overlapping intervals with a group ID

gintervals.covered_bp

Calculate total base pairs covered by intervals

gintervals.load

Loads a named intervals set

gintervals.neighbors

Finds neighbors between two sets of intervals

gintervals.load_chain

Loads assembly conversion table from a chain file

gintervals.is.bigset

Tests for big intervals set

Deletes a named intervals set

gintervals.mapply

Applies a function to values of track expressions

gintervals.rbind

Combines several sets of intervals

gintervals.union

Calculates a union of two sets of intervals

Returns a list of named intervals sets

gintervals.normalize

Normalize intervals to a fixed size

gintervals.liftover

Converts intervals from another assembly

Get reverse complement of DNA sequence

gintervals.update

Updates a named intervals set

giterator.intervals

Returns iterator intervals

gintervals.save

Creates a named intervals set

gintervals.quantiles

Calculates quantiles of a track expression for intervals

giterator.cartesian_grid

Creates a cartesian-grid iterator

Calculates quantiles of a track expression

gintervals.path

Returns the path on disk of an interval set

Partitions the values of track expression

gintervals.summary

Calculates summary statistics of track expression for intervals

Returns values from a lookup table based on track expression

gintervals.intersect

Calculates an intersection of two sets of intervals

gintervals.2d.all

Returns 2D intervals that cover the whole genome

gintervals.import_genes

Imports genes and annotations from files

Score DNA sequences with a k-mer over a region of interest

Returns samples from the values of track expression

Complement DNA sequence

gtrack.array.import

Creates an array track from array tracks or files

Finds intervals that match track expression

gtrack.2d.import

Creates a 2D track from tab-delimited file

gtrack.create_dirs

Create directories needed for track creation

gtrack.array.get_colnames

Returns column names of array track

Returns DNA sequences

Converts a track to the most current format

gtrack.attr.set

Assigns value to a track attribute

Divides track expression into segments

gtrack.2d.create

Creates a 'Rectangles' track from intervals and values

gintervals.random

Generate random genome intervals

Score DNA sequences with a PWM over a region of interest

Get reverse complement of DNA sequence

gtrack.create_dense

Creates a 'Dense' track from intervals and values

gtrack.2d.import_contacts

Creates a track from a file of inter-genomic contacts

gtrack.array.extract

Returns values from 'Array' track

gtrack.import_set

Creates one or more tracks from multiple WIG / BigWig / BedGraph / tab-delimited files on disk or FTP

Reverse DNA sequence

gtrack.import_mappedseq

Creates a track from a file of mapped sequences

gtrack.convert_to_indexed

Convert a track to indexed format

Returns information about a track

Calculates summary statistics of track expression

gtrack.liftover

Imports a track from another assembly

Creates a track from a track expression

gtrack.attr.export

Returns track attributes values

gtrack.array.set_colnames

Sets column names of array track

Returns a list of track names

Returns value of a track variable

Creates a new track from a lookup table based on track expression

gtrack.create_sparse

Creates a 'Sparse' track from intervals and values

gtrack.attr.import

Imports track attributes values

Modifies track contents

gtrack.attr.get

Returns value of a track attribute

Creates a track from WIG / BigWig / BedGraph / BED / tab-delimited file

Returns a list of track variables for a track

Assigns value to a track variable

Tests for a track existence

Creates a new virtual track

Deletes a track variable

gvtrack.array.slice

Defines rules for a single value calculation of a virtual 'Array' track

Creates a new track from smoothed values of track expression

gtrack.create_pwm_energy

Creates a new track from PSSM energy function

Attach or clear a genomic mask filter on a virtual track

Returns the path on disk of a track

Toolkit for analysis of genomic data

Deletes a track

Returns a list of virtual track names

Downloads files from FTP server

gvtrack.iterator

Defines modification rules for a one-dimensional iterator in a virtual track

Deletes a virtual track

Returns the definition of a virtual track

gvtrack.iterator.2d

Defines modification rules for a two-dimensional iterator in a virtual track

Calculates Wilcoxon test on sliding windows over track expression

gdb.create_genome

Create and Load a Genome Database

Creates a new Genomic Database

gintervals.neighbors.upstream

Directional neighbor finding functions

An environment for storing the package global variables

Calculates summary statistics of a track expression for bins

Changes current working directory in Genomic Database

gdb.convert_to_indexed

Change Database to Indexed Genome Format

Deletes a directory from Genomic Database

gbins.quantiles

Calculates quantiles of a track expression for bins

gcompute_strands_autocorr

Computes auto-correlation between the strands for a file of mapped sequences

Creates a new directory in Genomic Database

Calculates distribution of contact distances

Runs R commands on a cluster

Reloads database from the disk

Initializes connection with Genomic Database

gdb.get_readonly_attrs

Returns a list of read-only track attributes

gdb.set_readonly_attrs

Sets read-only track attributes

Returns the current working directory in Genomic Database

gdb.mark_cache_dirty

Mark cached track list as dirty