R: Toolkit for Analysis of Genomic Data

# Toolkit for Analysis of Genomic Data

## Documentation for package ‘misha’ version 5.11.23

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

G M P

misha-package | Toolkit for analysis of genomic data

## -- G --

gbins.quantiles | Calculates quantiles of a track expression for bins
gbins.summary | Calculates summary statistics of a track expression for bins
gcis_decay | Calculates distribution of contact distances
gcluster.run | Runs R commands on a cluster
gcompute_strands_autocorr | Computes auto-correlation between the strands for a file of mapped sequences
gcor | Calculates correlation between track expressions
gdataset.example_path | Create an example dataset on the fly
gdataset.info | Get dataset information
gdataset.load | Load a dataset into the namespace
gdataset.ls | List working database and loaded datasets
gdataset.save | Save a dataset
gdataset.unload | Unload a dataset from the namespace
gdb.build_genome | Build a misha genome database from a name
gdb.convert_to_indexed | Change Database to Indexed Genome Format
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.export_fasta | Export a database genome as FASTA
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 | Initializes connection with Genomic Database
gdb.init.examples | Initialise the example 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
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
gdist | Calculates distribution of track expressions
gextract | Returns evaluated track expression
ggenome.implant | Implant donor sequences into a reference genome
ggenome.transplant | Transplant sequences from one genome into another
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.convert_to_indexed | Convert 2D interval set to indexed format
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.annotate | Annotates 1D intervals using nearest neighbors
gintervals.as_chain | Transforms existing intervals to a chain format
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.chrom_sizes | Returns number of intervals per chromosome
gintervals.convert_to_indexed | Convert 1D interval set to indexed format
gintervals.coverage_fraction | Calculate fraction of genomic space covered by intervals
gintervals.covered_bp | Calculate total base pairs 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.import_bed | Import intervals from a BED file
gintervals.import_genes | Imports genes and annotations from files
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.ls | Returns a list of named intervals sets
gintervals.mapply | Applies a function to values of track expressions
gintervals.mark_overlaps | Mark overlapping intervals with a group ID
gintervals.neighbors | Finds neighbors between two sets of intervals
gintervals.neighbors.directional | Directional neighbor finding functions
gintervals.neighbors.downstream | Directional neighbor finding functions
gintervals.neighbors.upstream | Directional neighbor finding functions
gintervals.normalize | Normalize intervals to fixed or variable sizes
gintervals.path | Returns the path on disk of an interval set
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
giterator.cartesian_grid | Creates a cartesian-grid iterator
giterator.intervals | Returns iterator intervals
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
grevcomp | Get reverse complement of DNA sequence
gsample | Returns samples from the values of track expression
gscreen | Finds intervals that match track expression
gsegment | Divides track expression into segments
gseq.comp | Complement DNA sequence
gseq.extract | Returns DNA sequences
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.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.read_homer | Read motifs from a HOMER motif format file
gseq.read_jaspar | Read motifs from a JASPAR PFM format file
gseq.read_meme | Read motifs from a MEME minimal motif format file
gseq.rev | Reverse DNA sequence
gseq.revcomp | Get reverse complement of DNA sequence
gsetroot | Initializes connection with Genomic Database
gsummary | Calculates summary statistics of track expression
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.convert | Convert a legacy RDS gsynth model to .gsm format
gsynth.forbid_kmer | Forbid a k-mer pattern in a trained gsynth model
gsynth.load | Load a gsynth.model from disk
gsynth.random | Generate random genome sequences
gsynth.replace_kmer | Iteratively replace a k-mer in the genome
gsynth.sample | Sample a synthetic genome from a trained Markov model
gsynth.save | Save a gsynth.model to disk in .gsm format
gsynth.score | Score the genome under a trained gsynth model
gsynth.train | Train a stratified Markov model from genome sequences
gtrack.2d.convert_to_indexed | Convert 2D track to indexed format
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.convert_to_indexed | Convert a track to indexed format
gtrack.copy | Copies one or more tracks
gtrack.create | Creates a track from a track expression
gtrack.create_dense | Creates a 'Dense' track from intervals and values
gtrack.create_dirs | Create directories needed for track creation
gtrack.create_pwm_energy | Creates a new track from PSSM energy function
gtrack.create_sparse | Creates a 'Sparse' track from intervals and values
gtrack.dataset | Returns the database/dataset path for a track
gtrack.dbs | Returns the database paths that contain track(s)
gtrack.exists | Tests for a track existence
gtrack.export_bedgraph | Export a track to bedGraph format
gtrack.export_bigwig | Export a track to BigWig format
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.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.path | Returns the path on disk of a track
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
gvtrack.array.slice | Defines rules for a single value calculation of a virtual 'Array' track
gvtrack.clear | Deletes all virtual tracks
gvtrack.create | Creates a new virtual track
gvtrack.filter | Attach or clear a genomic mask filter on a 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
gwget | Downloads files from FTP server
gwilcox | Calculates Wilcoxon test on sliding windows over track expression

## -- M --

misha | Toolkit for analysis of genomic data

## -- P --

print.gsynth.model | Print summary of a gsynth.model