Learn R Programming

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

Copy Link

Version

Install

install.packages('misha')

Monthly Downloads

175

Version

4.3.12

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

August 31st, 2025

Functions in misha (4.3.12)

Deletes a directory from Genomic Database

Returns evaluated track expression

Calculates distribution of track expressions

Reloads database from the disk

Changes current working directory in Genomic Database

Creates a new directory in Genomic Database

gdb.set_readonly_attrs

Sets read-only track attributes

Creates a set of 2D intervals

gintervals.annotate

Annotates 1D intervals using nearest neighbors

gintervals.2d.all

Returns 2D intervals that cover the whole genome

Returns the current working directory in Genomic Database

gintervals.chrom_sizes

Returns number of intervals per chromosome

gintervals.exists

Tests for a named intervals set existence

gintervals.2d.band_intersect

Intersects two-dimensional intervals with a band

Creates a set of 1D intervals

gintervals.normalize

Normalize intervals to a fixed size

gintervals.quantiles

Calculates quantiles of a track expression for intervals

gintervals.mapply

Applies a function to values of track expressions

gintervals.canonic

Converts intervals to canonic form

gintervals.import_genes

Imports genes and annotations from files

gintervals.union

Calculates a union of two sets of intervals

gintervals.update

Updates a named intervals set

Deletes a named intervals set

gintervals.diff

Calculates difference of two intervals sets

gintervals.force_range

Limits intervals to chromosomal range

Returns values from a lookup table based on track expression

gintervals.neighbors

Finds neighbors between two sets of intervals

gintervals.summary

Calculates summary statistics of track expression for intervals

giterator.cartesian_grid

Creates a cartesian-grid iterator

Returns samples from the values of track expression

Partitions the values of track expression

gintervals.rbind

Combines several sets of intervals

gintervals.load

Loads a named intervals set

gintervals.save

Creates a named intervals set

gtrack.2d.import

Creates a 2D track from tab-delimited file

Returns 1D intervals that cover the whole genome

Calculates summary statistics of track expression

gintervals.load_chain

Loads assembly conversion table from a chain file

Returns a list of named intervals sets

giterator.intervals

Returns iterator intervals

Get reverse complement of DNA sequence

gtrack.attr.import

Imports track attributes values

gtrack.array.get_colnames

Returns column names of array track

gintervals.is.bigset

Tests for big intervals set

gtrack.attr.export

Returns track attributes values

Returns DNA sequences

gtrack.2d.create

Creates a 'Rectangles' track from intervals and values

Finds intervals that match track expression

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.array.set_colnames

Sets column names of array track

gintervals.intersect

Calculates an intersection of two sets of intervals

gintervals.liftover

Converts intervals from another assembly

gtrack.attr.get

Returns value of a track attribute

Divides track expression into segments

Creates a track from a track expression

gtrack.2d.import_contacts

Creates a track from a file of inter-genomic contacts

gtrack.attr.set

Assigns value to a track attribute

Calculates quantiles of a track expression

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

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

gtrack.liftover

Imports a track from another assembly

gtrack.create_sparse

Creates a 'Sparse' track from intervals and values

Returns information about a track

gtrack.create_dirs

Create directories needed for track creation

Tests for a track existence

gtrack.create_pwm_energy

Creates a new track from PSSM energy function

gtrack.create_dense

Creates a 'Dense' track from intervals and values

Deletes a track variable

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

Creates a new track from smoothed values of track expression

Modifies track contents

Assigns value to a track variable

Returns value of a track variable

Deletes a track

Returns a list of track names

gvtrack.array.slice

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

Deletes a virtual track

gvtrack.iterator

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

Returns a list of track variables for a track

Calculates Wilcoxon test on sliding windows over track expression

Returns the definition of a virtual track

gvtrack.iterator.2d

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

Returns a list of virtual track names

Downloads files from FTP server

Toolkit for analysis of genomic data

Creates a new virtual track

gbins.quantiles

Calculates quantiles of a track expression for bins

gdb.create_genome

Create and Load a Genome Database

An environment for storing the package global variables

Calculates distribution of contact distances

gcompute_strands_autocorr

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

Initializes connection with Genomic Database

gdb.get_readonly_attrs

Returns a list of read-only track attributes

Calculates summary statistics of a track expression for bins

Runs R commands on a cluster

Creates a new Genomic Database