Man pages for misha
Toolkit for Analysis of Genomic Data
| directional-neighbors | Directional neighbor finding functions |
| dot-misha | An environment for storing the package global variables |
| 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... |
| 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.get_readonly_attrs | Returns a list of read-only track attributes |
| gdb.info | Get Database Information |
| gdb.init | Initializes connection with Genomic Database |
| 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 |
| 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 |
| 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.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.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.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.import_genes | Imports genes and annotations from files |
| 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.normalize | Normalize intervals to a fixed size |
| 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... |
| 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.pwm | Score DNA sequences with a PWM over a region of interest |
| gseq.rev | Reverse DNA sequence |
| gseq.revcomp | Get reverse complement of DNA sequence |
| gsummary | Calculates summary statistics of track expression |
| 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.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.exists | Tests for a track existence |
| gtrack.import | Creates a track from WIG / BigWig / BedGraph / BED /... |
| gtrack.import_mappedseq | Creates a track from a file of mapped sequences |
| gtrack.import_set | Creates one or more tracks from multiple WIG / BigWig /... |
| 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... |
| gtrack.ls | Returns a list of track names |
| gtrack.modify | Modifies track contents |
| 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... |
| 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... |
| gvtrack.iterator.2d | Defines modification rules for a two-dimensional iterator in... |
| 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... |
| misha-package | Toolkit for analysis of genomic data |
| pipe | Pipe operator |
