Package index • misha

Track functions

Functions to manipulate and create tracks

gtrack.2d.create(): Creates a 'Rectangles' track from intervals and values
gtrack.2d.import(): Creates a 2D track from tab-delimited file
gtrack.2d.import_contacts(): Creates a track from a file of inter-genomic contacts
gtrack.array.extract(): Returns values from 'Array' track
gtrack.array.get_colnames(): Returns column names of array track
gtrack.array.import(): Creates an array track from array tracks or files
gtrack.array.set_colnames(): Sets column names of array track
gtrack.attr.export(): Returns track attributes values
gtrack.attr.get(): Returns value of a track attribute
gtrack.attr.import(): Imports track attributes values
gtrack.attr.set(): Assigns value to a track attribute
gtrack.convert(): Converts a track to the most current format
gtrack.create(): Creates a track from a track expression
gtrack.create_pwm_energy(): Creates a new track from PSSM energy function
gtrack.create_sparse(): Creates a 'Sparse' track from intervals and values
gtrack.create_dense(): Creates a 'Dense' track from intervals and values
gtrack.create_dirs(): Create directories needed for track creation
gtrack.dbs(): Returns the database paths that contain track(s)
gtrack.dataset(): Returns the database/dataset path for a track
gtrack.exists(): Tests for a track existence
gtrack.import(): Creates a track from WIG / BigWig / BedGraph / BED / tab-delimited file
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
gtrack.info(): Returns information about a track
gtrack.path(): Returns the path on disk of a track
gtrack.liftover(): Imports a track from another assembly
gtrack.lookup(): Creates a new track from a lookup table based on track expression
gtrack.ls(): Returns a list of track names
gtrack.modify(): Modifies track contents
gtrack.mv(): Renames or moves a track
gtrack.copy(): Copies one or more tracks
gtrack.rm(): Deletes a track
gtrack.smooth(): Creates a new track from smoothed values of track expression
gtrack.var.get(): Returns value of a track variable
gtrack.var.ls(): Returns a list of track variables for a track
gtrack.var.rm(): Deletes a track variable
gtrack.var.set(): Assigns value to a track variable
gtrack.convert_to_indexed(): Convert a track to indexed format
gtrack.2d.convert_to_indexed(): Convert 2D track to indexed format

Virtual track functions

Functions to manipulate and create virtual tracks

gvtrack.array.slice(): Defines rules for a single value calculation of a virtual 'Array' track
gvtrack.create(): Creates a new virtual track
gvtrack.info(): Returns the definition of a virtual track
gvtrack.iterator(): Defines modification rules for a one-dimensional iterator in a virtual track
gvtrack.iterator.2d(): Defines modification rules for a two-dimensional iterator in a virtual track
gvtrack.ls(): Returns a list of virtual track names
gvtrack.rm(): Deletes a virtual track
gvtrack.clear(): Deletes all virtual tracks
gvtrack.filter(): Attach or clear a genomic mask filter on a virtual track

Intervals functions

Functions to manipulate and create intervals

gintervals(): Creates a set of 1D intervals
gintervals.2d(): Creates a set of 2D intervals
gintervals.2d.all(): Returns 2D intervals that cover the whole genome
gintervals.2d.band_intersect(): Intersects two-dimensional intervals with a band
gintervals.2d.intersect(): Intersects two sets of 2D intervals
gintervals.2d.union(): Unites two sets of 2D intervals
gintervals.all(): Returns 1D intervals that cover the whole genome
gintervals.attr.export(): Returns interval set attributes values
gintervals.attr.get(): Returns value of an interval set attribute
gintervals.attr.import(): Imports interval set attributes values
gintervals.attr.set(): Assigns value to an interval set attribute
gintervals.canonic(): Converts intervals to canonic form
gintervals.mark_overlaps(): Mark overlapping intervals with a group ID
gintervals.chrom_sizes(): Returns number of intervals per chromosome
gintervals.covered_bp(): Calculate total base pairs covered by intervals
gintervals.coverage_fraction(): Calculate fraction of genomic space covered by intervals
gintervals.dataset(): Returns the database/dataset path for interval sets
gintervals.dbs(): Returns all database paths containing an interval set
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.from_mat(): Convert an interval-indexed matrix back to an intervals + values data.frame
gintervals.from_strings(): Creates 1D intervals from coordinate strings
gintervals.normalize(): Normalize intervals to fixed or variable sizes
gintervals.annotate(): Annotates 1D intervals using nearest neighbors
gintervals.import_genes(): Imports genes and annotations from files
gintervals.import_bed(): Import intervals from a BED file
gintervals.import_gff(): Import intervals from a GFF/GTF file
gintervals.import_vcf(): Import intervals from a VCF file
gintervals.intersect(): Calculates an intersection of two sets of intervals
gintervals.is.bigset(): Tests for big intervals set
gintervals.liftover(): Converts intervals from another assembly
gintervals.load(): Loads a named intervals set
gintervals.load_chain(): Loads assembly conversion table from a chain file
gintervals.as_chain(): Transforms existing intervals to a chain format
gintervals.path(): Returns the path on disk of an interval set
gintervals.ls(): Returns a list of named intervals sets
gintervals.mapply(): Applies a function to values of track expressions
gintervals.neighbors(): Finds neighbors between two sets of intervals
gintervals.neighbors.upstream() gintervals.neighbors.downstream() gintervals.neighbors.directional(): Directional neighbor finding functions
gintervals.quantiles(): Calculates quantiles of a track expression for intervals
gintervals.random(): Generate random genome intervals
gintervals.rbind(): Combines several sets of intervals
gintervals.rm(): Deletes a named intervals set
gintervals.save(): Creates a named intervals set
gintervals.summary(): Calculates summary statistics of track expression for intervals
gintervals.to_mat(): Convert intervals + values data.frame to an interval-indexed matrix
gintervals.union(): Calculates a union of two sets of intervals
gintervals.update(): Updates a named intervals set
gintervals.2d.convert_to_indexed(): Convert 2D interval set to indexed format
gintervals.convert_to_indexed(): Convert 1D interval set to indexed format
giterator.cartesian_grid(): Creates a cartesian-grid iterator
giterator.intervals(): Returns iterator intervals

Data manipulation functions

gdist(): Calculates distribution of track expressions
gbins.quantiles(): Calculates quantiles of a track expression for bins
gbins.summary(): Calculates summary statistics of a track expression for bins
gcor(): Calculates correlation between track expressions
gcis_decay(): Calculates distribution of contact distances
gcompute_strands_autocorr(): Computes auto-correlation between the strands for a file of mapped sequences
gextract(): Returns evaluated track expression
glookup(): Returns values from a lookup table based on track expression
gpartition(): Partitions the values of track expression
gquantiles(): Calculates quantiles of a track expression
gsample(): Returns samples from the values of track expression
gscreen(): Finds intervals that match track expression
gsegment(): Divides track expression into segments
gsummary(): Calculates summary statistics of track expression

Sequence functions

gseq.extract(): Returns DNA sequences
gseq.pwm(): Score DNA sequences with a PWM over a region of interest
gseq.pwm_edits(): Show optimal edits to reach a PWM score threshold
gseq.kmer(): Score DNA sequences with a k-mer over a region of interest
gseq.kmer.dist(): Compute k-mer distribution in genomic intervals
gseq.revcomp(): Get reverse complement of DNA sequence
grevcomp(): Get reverse complement of DNA sequence
gseq.rev(): Reverse DNA sequence
gseq.comp(): Complement DNA sequence

Track export

Functions to export tracks to standard genomic file formats

gtrack.export_bedgraph(): Export a track to bedGraph format
gtrack.export_bigwig(): Export a track to BigWig format

Motif import

Functions to import motifs from standard motif format files

gseq.read_meme(): Read motifs from a MEME minimal motif format file
gseq.read_jaspar(): Read motifs from a JASPAR PFM format file
gseq.read_homer(): Read motifs from a HOMER motif format file

Synthetic genome functions

Generate synthetic genomes using stratified Markov models

gsynth.train(): Train a stratified Markov model from genome sequences
gsynth.sample(): Sample a synthetic genome from a trained Markov model
gsynth.score(): Score the genome under a trained gsynth model
gsynth.random(): Generate random genome sequences
gsynth.replace_kmer(): Iteratively replace a k-mer in the genome
gsynth.save(): Save a gsynth.model to disk in .gsm format
gsynth.load(): Load a gsynth.model from disk
gsynth.convert(): Convert a legacy RDS gsynth model to .gsm format
gsynth.bin_map(): Create a bin mapping from value-based merge specifications
gsynth.cell_merge(): Resolve a cell-level merge specification into flat bin indices
gsynth.forbid_kmer(): Forbid a k-mer pattern in a trained gsynth model
print(<gsynth.model>): Print summary of a gsynth.model

Genome editing functions

Replace intervals in a reference genome with donor sequences

ggenome.implant(): Implant donor sequences into a reference genome
ggenome.transplant(): Transplant sequences from one genome into another

Database functions

gdb.build_genome(): Build a misha genome database from a name
gdb.create(): Creates a new Genomic Database
gdb.create_genome(): Create and Load a Genome Database
gdb.create_linked(): Create a linked database with symlinks to a parent database
gdb.genome_info(): Inspect a resolved genome recipe without building
gdb.get_readonly_attrs(): Returns a list of read-only track attributes
gdb.info(): Get Database Information
gdb.init() gsetroot(): Initializes connection with Genomic Database
gdb.init_examples(): Initialise the example Genomic Database
gdb.install_gff3_converter(): Pre-install UCSC's gff3ToGenePred binary
gdb.install_gtf_converter(): Pre-install UCSC's gtfToGenePred binary
gdb.install_intervals(): Install interval sets onto an existing groot
gdb.list_genomes(): List resolvable genome names
gdb.mark_cache_dirty(): Mark cached track list as dirty
gdb.reload(): Reloads database from the disk
gdb.set_readonly_attrs(): Sets read-only track attributes
gdb.unload(): Unloads the genome database
gdb.convert_to_indexed(): Change Database to Indexed Genome Format
gdb.export_fasta(): Export a database genome as FASTA
gdir.cd(): Changes current working directory in Genomic Database
gdir.create(): Creates a new directory in Genomic Database
gdir.cwd(): Returns the current working directory in Genomic Database
gdir.rm(): Deletes a directory from Genomic Database

Dataset functions

Functions for managing datasets (multiple data sources)

gdataset.load(): Load a dataset into the namespace
gdataset.unload(): Unload a dataset from the namespace
gdataset.save(): Save a dataset
gdataset.ls(): List working database and loaded datasets
gdataset.info(): Get dataset information
gdataset.example_path(): Create an example dataset on the fly

Other functions

Other

misha-package misha: Toolkit for analysis of genomic data
gcluster.run(): Runs R commands on a cluster
gwget(): Downloads files from FTP server
gwilcox(): Calculates Wilcoxon test on sliding windows over track expression