package biotk

You can search for identifiers within the package.

in-package search v0.2.0

biotk
- Biotk
  - Alphabet
    
    Make
    
    X
    
    S
  - Amino_acid
  - Bai
  - Bam
    
    Alignment0
    
    Header
  - Bam_iterator
  - Bed
    
    Bed3
    
    Item
    
    Bed4
    
    Item
    
    Bed5
    
    Item
    
    Bed6
    
    Item
    
    Item
    
    S
  - Bgzf
  - Cisbp
    
    Motif
    
    TF_information
  - Dataframe
    
    Ez
    
    Parser
  - Dna_sequence
    
    Parser
    
    Parser_of_char
    
    P
  - Encode
    
    Experiment_list
  - Fasta
  - Fastq
    
    Stats
  - FeatureCounts
    
    Summary
    
    Tsv
    
    Fields
    
    Direct
  - GAnnot
    
    LAssoc
    
    LMap
    
    LSet
    
    Selection
  - GLoc
  - Gcf
  - Gene
    
    Transcript
  - Gff
    
    Annotation
    
    GFF2
    
    GFF3
    
    Record
  - ISet
  - Idr
    
    Broad_output
    
    Row
    
    Narrow_output
    
    Row
  - Igv
    
    Statement
    
    proxy
  - Interval_tree
  - Interval_union
  - Jaspar
  - Let_syntax
    
    Result
  - Line
  - Line_oriented
    
    Item
    
    Make
    
    Item
    
    Parser
    
    S
  - List1
  - Macs
    
    Xls
  - Macs2
    
    Broad_peaks
    
    Xls
  - Meme
    
    Motif_format
  - Misc
  - NarrowPeak
    
    Item
  - Ncbi_genome
    
    Assembly_summary
  - Nucleotide
  - Phred_score
  - Phylo_tree_draw
  - Profile_matrix
    
    DNA
    
    Make
    
    A
    
    Protein
    
    S
  - Pwm
  - Pwm_stats
    
    TFM_pvalue
  - RanT
  - Range
  - Sam
    
    Flags
  - Solexa_score
  - Ucsc_genome_browser
    
    Chrom_size
    
    Fields
    
    Direct
  - Utils
  - Wfa
    
    Make
    
    Profile
    
    Score
    
    Symbol
    
    Nucleotide
    
    Nucleotide_IUPAC
    
    Nucleotide_frequency
    
    PSSM
    
    Profile
    
    S
    
    Score
    
    Symbol
biotk.croquis
- Biotk_croquis
  - Croquis
    
    Colormap
    
    Font
    
    Plot
  - Font_data
    
    Internal
  - Vg_text
    
    Font
    
    Layout
biotk.pipes
- Biotk_pipes
  - Pipe
    
    Make
    
    M
    
    Monad_infix
    
    Monad
    
    S
    
    Monad_infix
biotk.pipes.unix
- Biotk_pipes_unix
  - Pipe
    
    Monad_infix

Legend:
Library
Module
Module type
Parameter
Class
Class type

BED format

BED (Browser Extensible Data) format is used to describe a collection of genomic features. It is a tabulated format. See the {https://genome.ucsc.edu/FAQ/FAQformat.html#format1specification

}

. Several variants exist, depending on the number of fields, and they are accordingly named BED3, BED4, etc. This module offers one representation per variant, including a general-purpose representation only assuming 3 fields.

type strand = [

| `Plus
| `Minus
| `Not_relevant
| `Unknown

]

val parse_strand : string -> (strand, string) Stdlib.result

val unparse_strand : strand -> string

module type Item = sig ... end

module type S = sig ... end

module Item : Item with type t = GLoc.t * string list

include S with type item := Item.t

val load : string -> Item.t list

val load_as_lmap : string -> Item.t GAnnot.LMap.t

val save : Item.t list -> string -> unit

module Bed3 : sig ... end

module Bed4 : sig ... end

module Bed5 : sig ... end

module Bed6 : sig ... end