Toolkit for Analysis of Genomic Data
Save a dataset
Unload a dataset from the namespace
Change Database to Indexed Genome Format
Create and Load a Genome Database
Create a linked database with symlinks to a parent database
Limits intervals to chromosomal range
Imports genes and annotations from files
Calculates an intersection of two sets of intervals
Tests for big intervals set
Converts intervals from another assembly
Loads assembly conversion table from a chain file
Loads a named intervals set
Returns a list of named intervals sets
Calculates summary statistics of track expression for intervals
Calculates a union of two sets of intervals
Updates a named intervals set
Returns values from 'Array' track
Returns column names of array track
Creates an array track from array tracks or files
Sets column names of array track
Returns track attributes values
Returns value of a track attribute
Imports track attributes values
Assigns value to a track attribute
Convert a track to indexed format
Converts a track to the most current format
Copies a track
Creates a 'Dense' track from intervals and values
Create directories needed for track creation
Creates a new track from PSSM energy function
Creates a 'Sparse' track from intervals and values
Defines modification rules for a two-dimensional iterator in a virtual...
Creates a new directory in Genomic Database
Returns the current working directory in Genomic Database
Deletes a directory from Genomic Database
Calculates distribution of track expressions
Returns evaluated track expression
Returns 2D intervals that cover the whole genome
Intersects two-dimensional intervals with a band
Returns number of intervals per chromosome
Tests for a named intervals set existence
Returns DNA sequences
List working database and loaded datasets
Directional neighbor finding functions
An environment for storing the package global variables
Calculates quantiles of a track expression for bins
Calculates summary statistics of a track expression for bins
Calculates distribution of contact distances
Changes current working directory in Genomic Database
Runs R commands on a cluster
Computes auto-correlation between the strands for a file of mapped seq...
Calculates correlation between track expressions
Create an example dataset on the fly
Get dataset information
Load a dataset into the namespace
Creates a new Genomic Database
Returns a list of read-only track attributes
Get Database Information
Initializes connection with Genomic Database
Mark cached track list as dirty
Reloads database from the disk
Sets read-only track attributes
Convert 2D interval set to indexed format
Creates a set of 2D intervals
Returns 1D intervals that cover the whole genome
Annotates 1D intervals using nearest neighbors
Transforms existing intervals to a chain format
Converts intervals to canonic form
Convert 1D interval set to indexed format
Calculate fraction of genomic space covered by intervals
Calculate total base pairs covered by intervals
Returns the database/dataset path for interval sets
Returns all database paths containing an interval set
Calculates difference of two intervals sets
Applies a function to values of track expressions
Mark overlapping intervals with a group ID
Finds neighbors between two sets of intervals
Normalize intervals to fixed or variable sizes
Returns the path on disk of an interval set
Calculates quantiles of a track expression for intervals
Generate random genome intervals
Combines several sets of intervals
Creates a set of 1D intervals
Deletes a named intervals set
Creates a named intervals set
Compute k-mer distribution in genomic intervals
Creates a cartesian-grid iterator
Returns iterator intervals
Returns values from a lookup table based on track expression
Partitions the values of track expression
Returns information about a track
Calculates quantiles of a track expression
Get reverse complement of DNA sequence
Returns samples from the values of track expression
Finds intervals that match track expression
Divides track expression into segments
Complement DNA sequence
Imports a track from another assembly
Score DNA sequences with a k-mer over a region of interest
Score DNA sequences with a PWM over a region of interest
Reverse DNA sequence
Get reverse complement of DNA sequence
Calculates summary statistics of track expression
Create a bin mapping from value-based merge specifications
Load a gsynth.model from disk
Print summary of a gsynth.model
Generate random genome sequences
Iteratively replace a k-mer in the genome
Sample a synthetic genome from a trained Markov model
Save a gsynth.model to disk
Train a stratified Markov-5 model from genome sequences
Creates a 'Rectangles' track from intervals and values
Creates a track from a file of inter-genomic contacts
Creates a 2D track from tab-delimited file
Creates a track from a track expression
Returns the database/dataset path for a track
Returns the database paths that contain track(s)
Tests for a track existence
Creates a track from a file of mapped sequences
Creates one or more tracks from multiple WIG / BigWig / BedGraph / tab...
Creates a track from WIG / BigWig / BedGraph / BED / tab-delimited fil...
Creates a new track from a lookup table based on track expression
Returns a list of track names
Modifies track contents
Renames or moves a track
Returns the path on disk of a track
Deletes a track
Creates a new track from smoothed values of track expression
Returns value of a track variable
Returns a list of track variables for a track
Deletes a track variable
Assigns value to a track variable
Defines rules for a single value calculation of a virtual 'Array' trac...
Creates a new virtual track
Attach or clear a genomic mask filter on a virtual track
Returns the definition of a virtual track
Defines modification rules for a one-dimensional iterator in a virtual...
Returns a list of virtual track names
Deletes a virtual track
Downloads files from FTP server
Calculates Wilcoxon test on sliding windows over track expression
Toolkit for analysis of genomic data
Pipe operator
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>.
Useful links