misha/_pkgdown.yml at master · tanaylab/misha · GitHub

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reference:
  - title: Track functions
    desc:  Functions to manipulate and create tracks
    contents:
      - gtrack.2d.create
      - gtrack.2d.import
      - gtrack.2d.import_contacts
      - gtrack.array.extract
      - gtrack.array.get_colnames
      - gtrack.array.import
      - gtrack.array.set_colnames
      - gtrack.attr.export
      - gtrack.attr.get
      - gtrack.attr.import
      - gtrack.attr.set
      - gtrack.convert
      - gtrack.create
      - gtrack.create_pwm_energy
      - gtrack.create_sparse
      - gtrack.create_dense
      - gtrack.create_dirs
      - gtrack.dbs
      - gtrack.dataset
      - gtrack.exists
      - gtrack.import
      - gtrack.import_mappedseq
      - gtrack.import_set
      - gtrack.info
      - gtrack.path
      - gtrack.liftover
      - gtrack.lookup
      - gtrack.ls
      - gtrack.modify
      - gtrack.mv
      - gtrack.copy
      - gtrack.rm
      - gtrack.smooth
      - gtrack.var.get
      - gtrack.var.ls
      - gtrack.var.rm
      - gtrack.var.set
      - gtrack.convert_to_indexed
      - gtrack.2d.convert_to_indexed
  - title: Virtual track functions
    desc:  Functions to manipulate and create virtual tracks
    contents:
      - gvtrack.array.slice
      - gvtrack.create
      - gvtrack.info
      - gvtrack.iterator
      - gvtrack.iterator.2d
      - gvtrack.ls
      - gvtrack.rm
      - gvtrack.filter
  - title: Intervals functions
    desc:  Functions to manipulate and create intervals
    contents:
      - gintervals
      - gintervals.2d
      - gintervals.2d.all
      - gintervals.2d.band_intersect
      - gintervals.all
      - gintervals.attr.export
      - gintervals.attr.get
      - gintervals.attr.import
      - gintervals.attr.set
      - gintervals.canonic
      - gintervals.mark_overlaps
      - gintervals.chrom_sizes
      - gintervals.covered_bp
      - gintervals.coverage_fraction
      - gintervals.dataset
      - gintervals.dbs
      - gintervals.diff
      - gintervals.exists
      - gintervals.force_range
      - gintervals.normalize
      - gintervals.annotate
      - gintervals.import_genes
      - gintervals.intersect
      - gintervals.is.bigset
      - gintervals.liftover
      - gintervals.load
      - gintervals.load_chain
      - gintervals.as_chain
      - gintervals.path
      - gintervals.ls
      - gintervals.mapply
      - gintervals.neighbors
      - gintervals.neighbors.upstream
      - gintervals.neighbors.downstream
      - gintervals.neighbors.directional
      - gintervals.quantiles
      - gintervals.random
      - gintervals.rbind
      - gintervals.rm
      - gintervals.save
      - gintervals.summary
      - gintervals.union
      - gintervals.update
      - gintervals.2d.convert_to_indexed
      - gintervals.convert_to_indexed
      - giterator.cartesian_grid
      - giterator.intervals
  - title: Data manipulation functions
    desc: Data manipulation functions
    contents:
      - gdist
      - gbins.quantiles
      - gbins.summary
      - gcor
      - gcis_decay
      - gcompute_strands_autocorr
      - gdist
      - gextract
      - glookup
      - gpartition
      - gquantiles
      - gsample
      - gscreen
      - gsegment
      - gsummary
  - title: Sequence functions
    desc: Sequence functions
    contents:
      - gseq.extract
      - gseq.pwm
      - gseq.pwm_edits
      - gseq.kmer
      - gseq.kmer.dist
      - gseq.revcomp
      - grevcomp
      - gseq.rev
      - gseq.comp
  - title: Track export
    desc: Functions to export tracks to standard genomic file formats
    contents:
      - gtrack.export_bedgraph
      - gtrack.export_bigwig
  - title: Motif import
    desc: Functions to import motifs from standard motif format files
    contents:
      - gseq.read_meme
      - gseq.read_jaspar
      - gseq.read_homer
  - title: Synthetic genome functions
    desc: Generate synthetic genomes using stratified Markov models
    contents:
      - gsynth.train
      - gsynth.sample
      - gsynth.random
      - gsynth.replace_kmer
      - gsynth.save
      - gsynth.load
      - gsynth.convert
      - gsynth.bin_map
      - print.gsynth.model
  - title: Genome editing functions
    desc: Replace intervals in a reference genome with donor sequences
    contents:
      - ggenome.implant
      - ggenome.transplant
  - title: Database functions
    desc: Database functions
    contents:
      - gdb.create
      - gdb.create_genome
      - gdb.create_linked
      - gdb.get_readonly_attrs
      - gdb.info
      - gdb.init
      - gdb.mark_cache_dirty
      - gdb.reload
      - gdb.set_readonly_attrs
      - gdb.convert_to_indexed
      - gdb.export_fasta
      - gdir.cd
      - gdir.create
      - gdir.cwd
      - gdir.rm
  - title: Dataset functions
    desc: Functions for managing datasets (multiple data sources)
    contents:
      - gdataset.load
      - gdataset.unload
      - gdataset.save
      - gdataset.ls
      - gdataset.info
      - gdataset.example_path
  - title: Other functions
    desc: Other
    contents:
      - misha-package
      - gcluster.run
      - gwget
      - gwilcox