This package is considered a duplicate. The official version of this package is found at:https://tanaylab.r-universe.dev/misha

Package: misha 4.3.6

Aviezer Lifshitz

misha: Toolkit for Analysis of Genomic Data

A toolkit for analysis of genomic data. The 'misha' package implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay (2011) <doi:10.1038/ng.947>.

Authors:Misha Hoichman [aut], Aviezer Lifshitz [aut, cre], Eitan Yaffe [aut], Amos Tanay [aut], Weizmann Institute of Science [cph]

misha_4.3.6.tar.gz
misha_4.3.6.tar.gz(r-4.5-noble)misha_4.3.6.tar.gz(r-4.4-noble)
misha.pdf |misha.html✨
misha/json (API)
NEWS

# Install 'misha' in R:

install.packages('misha', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tanaylab/misha/issues

Pkgdown site:https://tanaylab.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.00 score 71 downloads 98 exports 2 dependencies

Last updated 3 days agofrom:2700508720. Checks:1 OK, 2 NOTE. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 06 2025
R-4.5-linux-x86_64	NOTE	Mar 06 2025
R-4.4-linux-x86_64	NOTE	Mar 06 2025

Exports:.misha %>%gbins.quantiles gbins.summary gcis_decay gcluster.run gcompute_strands_autocorr gdb.create gdb.create_genome gdb.get_readonly_attrs gdb.init gdb.init_examples gdb.reload gdb.set_readonly_attrs gdir.cd gdir.create gdir.cwd gdir.rm gdist gextract gintervals gintervals.2d gintervals.2d.all gintervals.2d.band_intersect gintervals.all gintervals.canonic gintervals.chrom_sizes gintervals.diff gintervals.exists gintervals.force_range gintervals.import_genes gintervals.intersect gintervals.is.bigset gintervals.liftover gintervals.load gintervals.load_chain gintervals.ls gintervals.mapply gintervals.neighbors gintervals.quantiles gintervals.rbind gintervals.rm gintervals.save gintervals.summary gintervals.union gintervals.update giterator.cartesian_grid giterator.intervals glookup gpartition gquantiles grevcomp gsample gscreen gsegment gseq.extract gsetroot gsummary gtrack.2d.create gtrack.2d.import gtrack.2d.import_contacts gtrack.array.extract gtrack.array.get_colnames gtrack.array.import gtrack.array.set_colnames gtrack.attr.export gtrack.attr.get gtrack.attr.import gtrack.attr.set gtrack.convert gtrack.create gtrack.create_dirs gtrack.create_pwm_energy gtrack.create_sparse gtrack.exists gtrack.import gtrack.import_mappedseq gtrack.import_set gtrack.info gtrack.liftover gtrack.lookup gtrack.ls gtrack.modify gtrack.rm gtrack.smooth gtrack.var.get gtrack.var.ls gtrack.var.rm gtrack.var.set gvtrack.array.slice gvtrack.create gvtrack.info gvtrack.iterator gvtrack.iterator.2d gvtrack.ls gvtrack.rm gwget gwilcox

Dependencies:curl magrittr

Genomes

Rendered fromGenomes.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-03-06
Started: 2023-09-05

Manual

Rendered fromManual.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-03-06
Started: 2023-09-05

Citation

Readme and manuals

Help Manual

Help page	Topics
Toolkit for analysis of genomic data	misha-package misha
Calculates quantiles of a track expression for bins	gbins.quantiles
Calculates summary statistics of a track expression for bins	gbins.summary
Calculates distribution of contact distances	gcis_decay
Runs R commands on a cluster	gcluster.run
Computes auto-correlation between the strands for a file of mapped sequences	gcompute_strands_autocorr
Creates a new Genomic Database	gdb.create
Create and Load a Genome Database	gdb.create_genome
Returns a list of read-only track attributes	gdb.get_readonly_attrs
Reloads database from the disk	gdb.reload
Sets read-only track attributes	gdb.set_readonly_attrs
Changes current working directory in Genomic Database	gdir.cd
Creates a new directory in Genomic Database	gdir.create
Returns the current working directory in Genomic Database	gdir.cwd
Deletes a directory from Genomic Database	gdir.rm
Calculates distribution of track expressions	gdist
Returns evaluated track expression	gextract
Creates a set of 1D intervals	gintervals
Creates a set of 2D intervals	gintervals.2d
Returns 2D intervals that cover the whole genome	gintervals.2d.all
Intersects two-dimensional intervals with a band	gintervals.2d.band_intersect
Returns 1D intervals that cover the whole genome	gintervals.all
Converts intervals to canonic form	gintervals.canonic
Returns number of intervals per chromosome	gintervals.chrom_sizes
Calculates difference of two intervals sets	gintervals.diff
Tests for a named intervals set existence	gintervals.exists
Limits intervals to chromosomal range	gintervals.force_range
Imports genes and annotations from files	gintervals.import_genes
Calculates an intersection of two sets of intervals	gintervals.intersect
Tests for big intervals set	gintervals.is.bigset
Converts intervals from another assembly	gintervals.liftover
Loads a named intervals set	gintervals.load
Loads assembly conversion table from a chain file	gintervals.load_chain
Returns a list of named intervals sets	gintervals.ls
Applies a function to values of track expressions	gintervals.mapply
Finds neighbors between two sets of intervals	gintervals.neighbors
Calculates quantiles of a track expression for intervals	gintervals.quantiles
Combines several sets of intervals	gintervals.rbind
Deletes a named intervals set	gintervals.rm
Creates a named intervals set	gintervals.save
Calculates summary statistics of track expression for intervals	gintervals.summary
Calculates a union of two sets of intervals	gintervals.union
Updates a named intervals set	gintervals.update
Creates a cartesian-grid iterator	giterator.cartesian_grid
Returns iterator intervals	giterator.intervals
Returns values from a lookup table based on track expression	glookup
Partitions the values of track expression	gpartition
Calculates quantiles of a track expression	gquantiles
Get reverse complement of DNA sequence	grevcomp
Returns samples from the values of track expression	gsample
Finds intervals that match track expression	gscreen
Divides track expression into segments	gsegment
Returns DNA sequences	gseq.extract
Initializes connection with Genomic Database	gdb.init gdb.init.examples gdb.init_examples gsetroot
Calculates summary statistics of track expression	gsummary
Creates a 'Rectangles' track from intervals and values	gtrack.2d.create
Creates a 2D track from tab-delimited file	gtrack.2d.import
Creates a track from a file of inter-genomic contacts	gtrack.2d.import_contacts
Returns values from 'Array' track	gtrack.array.extract
Returns column names of array track	gtrack.array.get_colnames
Creates an array track from array tracks or files	gtrack.array.import
Sets column names of array track	gtrack.array.set_colnames
Returns track attributes values	gtrack.attr.export
Returns value of a track attribute	gtrack.attr.get
Imports track attributes values	gtrack.attr.import
Assigns value to a track attribute	gtrack.attr.set
Converts a track to the most current format	gtrack.convert
Creates a track from a track expression	gtrack.create
Create directories needed for track creation	gtrack.create_dirs
Creates a new track from PSSM energy function	gtrack.create_pwm_energy
Creates a 'Sparse' track from intervals and values	gtrack.create_sparse
Tests for a track existence	gtrack.exists
Creates a track from WIG / BigWig / BedGraph / tab-delimited file	gtrack.import
Creates a track from a file of mapped sequences	gtrack.import_mappedseq
Creates one or more tracks from multiple WIG / BigWig / BedGraph / tab-delimited files on disk or FTP	gtrack.import_set
Returns information about a track	gtrack.info
Imports a track from another assembly	gtrack.liftover
Creates a new track from a lookup table based on track expression	gtrack.lookup
Returns a list of track names	gtrack.ls
Modifies track contents	gtrack.modify
Deletes a track	gtrack.rm
Creates a new track from smoothed values of track expression	gtrack.smooth
Returns value of a track variable	gtrack.var.get
Returns a list of track variables for a track	gtrack.var.ls
Deletes a track variable	gtrack.var.rm
Assigns value to a track variable	gtrack.var.set
Defines rules for a single value calculation of a virtual 'Array' track	gvtrack.array.slice
Creates a new virtual track	gvtrack.create
Returns the definition of a virtual track	gvtrack.info
Defines modification rules for a one-dimensional iterator in a virtual track	gvtrack.iterator
Defines modification rules for a two-dimensional iterator in a virtual track	gvtrack.iterator.2d
Returns a list of virtual track names	gvtrack.ls
Deletes a virtual track	gvtrack.rm
Downloads files from FTP server	gwget
Calculates Wilcoxon test on sliding windows over track expression	gwilcox