| 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 |
| Calculates correlation between track expressions | gcor |
| Create an example dataset on the fly | gdataset.example_path |
| Get dataset information | gdataset.info |
| Load a dataset into the namespace | gdataset.load |
| List working database and loaded datasets | gdataset.ls |
| Save a dataset | gdataset.save |
| Unload a dataset from the namespace | gdataset.unload |
| Build a misha genome database from a name | gdb.build_genome |
| Change Database to Indexed Genome Format | gdb.convert_to_indexed |
| Creates a new Genomic Database | gdb.create |
| Create and Load a Genome Database | gdb.create_genome |
| Create a linked database with symlinks to a parent database | gdb.create_linked |
| Export a database genome as FASTA | gdb.export_fasta |
| Inspect a resolved genome recipe without building | gdb.genome_info |
| Returns a list of read-only track attributes | gdb.get_readonly_attrs |
| Get Database Information | gdb.info |
| Initializes connection with Genomic Database | gdb.init gsetroot |
| Initialise the example Genomic Database | gdb.init.examples gdb.init_examples |
| Pre-install UCSC's gff3ToGenePred binary | gdb.install_gff3_converter |
| Pre-install UCSC's gtfToGenePred binary | gdb.install_gtf_converter |
| Install interval sets onto an existing groot | gdb.install_intervals |
| List resolvable genome names | gdb.list_genomes |
| Mark cached track list as dirty | gdb.mark_cache_dirty |
| Reloads database from the disk | gdb.reload |
| Sets read-only track attributes | gdb.set_readonly_attrs |
| Unloads the genome database | gdb.unload |
| 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 |
| Implant donor sequences into a reference genome | ggenome.implant |
| Transplant sequences from one genome into another | ggenome.transplant |
| 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 |
| Convert 2D interval set to indexed format | gintervals.2d.convert_to_indexed |
| Intersects two sets of 2D intervals | gintervals.2d.intersect |
| Unites two sets of 2D intervals | gintervals.2d.union |
| Returns 1D intervals that cover the whole genome | gintervals.all |
| Annotates 1D intervals using nearest neighbors | gintervals.annotate |
| Transforms existing intervals to a chain format | gintervals.as_chain |
| Returns interval set attributes values | gintervals.attr.export |
| Returns value of an interval set attribute | gintervals.attr.get |
| Imports interval set attributes values | gintervals.attr.import |
| Assigns value to an interval set attribute | gintervals.attr.set |
| Converts intervals to canonic form | gintervals.canonic |
| Returns number of intervals per chromosome | gintervals.chrom_sizes |
| Convert 1D interval set to indexed format | gintervals.convert_to_indexed |
| Calculate fraction of genomic space covered by intervals | gintervals.coverage_fraction |
| Calculate total base pairs covered by intervals | gintervals.covered_bp |
| Returns the database/dataset path for interval sets | gintervals.dataset |
| Returns all database paths containing an interval set | gintervals.dbs |
| 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 |
| Convert an interval-indexed matrix back to an intervals + values data.frame | gintervals.from_mat |
| Creates 1D intervals from coordinate strings | gintervals.from_strings |
| Import intervals from a BED file | gintervals.import_bed |
| Imports genes and annotations from files | gintervals.import_genes |
| Import intervals from a GFF/GTF file | gintervals.import_gff |
| Import intervals from a VCF file | gintervals.import_vcf |
| 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 |
| Mark overlapping intervals with a group ID | gintervals.mark_overlaps |
| Finds neighbors between two sets of intervals | gintervals.neighbors |
| Directional neighbor finding functions | gintervals.neighbors.directional gintervals.neighbors.downstream gintervals.neighbors.upstream |
| Normalize intervals to fixed or variable sizes | gintervals.normalize |
| Returns the path on disk of an interval set | gintervals.path |
| Calculates quantiles of a track expression for intervals | gintervals.quantiles |
| Generate random genome intervals | gintervals.random |
| 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 |
| Convert intervals + values data.frame to an interval-indexed matrix | gintervals.to_mat |
| 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 |
| Complement DNA sequence | gseq.comp |
| Returns DNA sequences | gseq.extract |
| Score DNA sequences with a k-mer over a region of interest | gseq.kmer |
| Compute k-mer distribution in genomic intervals | gseq.kmer.dist |
| Score DNA sequences with a PWM over a region of interest | gseq.pwm |
| Show optimal edits to reach a PWM score threshold | gseq.pwm_edits |
| Read motifs from a HOMER motif format file | gseq.read_homer |
| Read motifs from a JASPAR PFM format file | gseq.read_jaspar |
| Read motifs from a MEME minimal motif format file | gseq.read_meme |
| Reverse DNA sequence | gseq.rev |
| Get reverse complement of DNA sequence | gseq.revcomp |
| Calculates summary statistics of track expression | gsummary |
| Create a bin mapping from value-based merge specifications | gsynth.bin_map |
| Resolve a cell-level merge specification into flat bin indices | gsynth.cell_merge |
| Convert a legacy RDS gsynth model to .gsm format | gsynth.convert |
| Forbid a k-mer pattern in a trained gsynth model | gsynth.forbid_kmer |
| Load a gsynth.model from disk | gsynth.load |
| Generate random genome sequences | gsynth.random |
| Iteratively replace a k-mer in the genome | gsynth.replace_kmer |
| Sample a synthetic genome from a trained Markov model | gsynth.sample |
| Save a gsynth.model to disk in .gsm format | gsynth.save |
| Score the genome under a trained gsynth model | gsynth.score |
| Train a stratified Markov model from genome sequences | gsynth.train |
| Convert 2D track to indexed format | gtrack.2d.convert_to_indexed |
| 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 |
| Convert a track to indexed format | gtrack.convert_to_indexed |
| Copies one or more tracks | gtrack.copy |
| Creates a track from a track expression | gtrack.create |
| Creates a 'Dense' track from intervals and values | gtrack.create_dense |
| 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 |
| Returns the database/dataset path for a track | gtrack.dataset |
| Returns the database paths that contain track(s) | gtrack.dbs |
| Tests for a track existence | gtrack.exists |
| Export a track to bedGraph format | gtrack.export_bedgraph |
| Export a track to BigWig format | gtrack.export_bigwig |
| Creates a track from WIG / BigWig / BedGraph / BED / 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 |
| Renames or moves a track | gtrack.mv |
| Returns the path on disk of a track | gtrack.path |
| 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 |
| Deletes all virtual tracks | gvtrack.clear |
| Creates a new virtual track | gvtrack.create |
| Attach or clear a genomic mask filter on a virtual track | gvtrack.filter |
| 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 |
| Print summary of a gsynth.model | print.gsynth.model |
