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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

252

Version

5.4.5

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

February 20th, 2026

Functions in misha (5.4.5)

Reloads database from the disk

gdb.mark_cache_dirty

Mark cached track list as dirty

gdb.set_readonly_attrs

Sets read-only track attributes

Changes current working directory in Genomic Database

gdb.convert_to_indexed

Change Database to Indexed Genome Format

Calculates distribution of track expressions

Deletes a directory from Genomic Database

Creates a new Genomic Database

gintervals.2d.convert_to_indexed

Convert 2D interval set to indexed format

Creates a set of 1D intervals

Creates a new directory in Genomic Database

Returns the current working directory in Genomic Database

gintervals.2d.band_intersect

Intersects two-dimensional intervals with a band

gintervals.2d.all

Returns 2D intervals that cover the whole genome

gintervals.as_chain

Transforms existing intervals to a chain format

gintervals.canonic

Converts intervals to canonic form

Returns evaluated track expression

Creates a set of 2D intervals

Get Database Information

gintervals.annotate

Annotates 1D intervals using nearest neighbors

Returns all database paths containing an interval set

gintervals.dataset

Returns the database/dataset path for interval sets

gintervals.force_range

Limits intervals to chromosomal range

gintervals.chrom_sizes

Returns number of intervals per chromosome

gintervals.convert_to_indexed

Convert 1D interval set to indexed format

gintervals.mark_overlaps

Mark overlapping intervals with a group ID

gintervals.import_genes

Imports genes and annotations from files

gintervals.normalize

Normalize intervals to fixed or variable sizes

gintervals.covered_bp

Calculate total base pairs covered by intervals

Initializes connection with Genomic Database

Returns 1D intervals that cover the whole genome

gintervals.coverage_fraction

Calculate fraction of genomic space covered by intervals

gintervals.random

Generate random genome intervals

gintervals.is.bigset

Tests for big intervals set

gintervals.mapply

Applies a function to values of track expressions

gintervals.exists

Tests for a named intervals set existence

gintervals.diff

Calculates difference of two intervals sets

gintervals.intersect

Calculates an intersection of two sets of intervals

gintervals.load_chain

Loads assembly conversion table from a chain file

gintervals.liftover

Converts intervals from another assembly

gintervals.neighbors

Finds neighbors between two sets of intervals

Returns a list of named intervals sets

gintervals.update

Updates a named intervals set

gintervals.rbind

Combines several sets of intervals

gintervals.union

Calculates a union of two sets of intervals

Get reverse complement of DNA sequence

giterator.cartesian_grid

Creates a cartesian-grid iterator

gintervals.summary

Calculates summary statistics of track expression for intervals

gintervals.path

Returns the path on disk of an interval set

gintervals.quantiles

Calculates quantiles of a track expression for intervals

Partitions the values of track expression

gintervals.load

Loads a named intervals set

gintervals.save

Creates a named intervals set

Deletes a named intervals set

Complement DNA sequence

giterator.intervals

Returns iterator intervals

Calculates quantiles of a track expression

Returns values from a lookup table based on track expression

Load a gsynth.model from disk

Create a bin mapping from value-based merge specifications

Returns samples from the values of track expression

Finds intervals that match track expression

Returns DNA sequences

gsynth.replace_kmer

Iteratively replace a k-mer in the genome

Divides track expression into segments

Generate random genome sequences

Reverse DNA sequence

Get reverse complement of DNA sequence

Score DNA sequences with a PWM over a region of interest

Calculates summary statistics of track expression

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

Compute k-mer distribution in genomic intervals

Sample a synthetic genome from a trained Markov model

Train a stratified Markov-5 model from genome sequences

Save a gsynth.model to disk

gtrack.create_dirs

Create directories needed for track creation

gtrack.convert_to_indexed

Convert a track to indexed format

gtrack.2d.import

Creates a 2D track from tab-delimited file

gtrack.2d.create

Creates a 'Rectangles' track from intervals and values

gtrack.array.get_colnames

Returns column names of array track

gtrack.attr.get

Returns value of a track attribute

gtrack.attr.import

Imports track attributes values

gtrack.2d.import_contacts

Creates a track from a file of inter-genomic contacts

Converts a track to the most current format

gtrack.array.extract

Returns values from 'Array' track

gtrack.array.import

Creates an array track from array tracks or files

gtrack.attr.export

Returns track attributes values

gtrack.attr.set

Assigns value to a track attribute

gtrack.create_dense

Creates a 'Dense' track from intervals and values

Tests for a track existence

Returns information about a track

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

Creates a track from a track expression

gtrack.array.set_colnames

Sets column names of array track

Creates a new track from smoothed values of track expression

gtrack.create_pwm_energy

Creates a new track from PSSM energy function

gtrack.import_mappedseq

Creates a track from a file of mapped sequences

Returns the database/dataset path for a track

Returns the database paths that contain track(s)

Deletes a track

Returns the path on disk of a track

gtrack.create_sparse

Creates a 'Sparse' track from intervals and values

Renames or moves a track

Deletes a track variable

Modifies track contents

gtrack.liftover

Imports a track from another assembly

Returns a list of track variables for a track

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

gtrack.import_set

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

Returns a list of track names

Assigns value to a track variable

Attach or clear a genomic mask filter on a virtual track

Downloads files from FTP server

Deletes a virtual track

Returns value of a track variable

gvtrack.array.slice

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

Creates a new virtual track

print.gsynth.model

Print summary of a gsynth.model

gvtrack.iterator.2d

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

Returns the definition of a virtual track

Toolkit for analysis of genomic data

Returns a list of virtual track names

Calculates Wilcoxon test on sliding windows over track expression

gvtrack.iterator

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

Calculates correlation between track expressions

gdataset.example_path

Create an example dataset on the fly

gintervals.neighbors.upstream

Directional neighbor finding functions

Get dataset information

gcompute_strands_autocorr

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

gdb.create_genome

Create and Load a Genome Database

gdataset.unload

Unload a dataset from the namespace

Runs R commands on a cluster

Calculates summary statistics of a track expression for bins

An environment for storing the package global variables

Calculates distribution of contact distances

Load a dataset into the namespace

gdb.create_linked

Create a linked database with symlinks to a parent database

gbins.quantiles

Calculates quantiles of a track expression for bins

gdb.export_fasta

Export a database genome as FASTA

gdb.get_readonly_attrs

Returns a list of read-only track attributes

List working database and loaded datasets