package biotk

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in-package search v0.2.0

package biotk

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

module Transcript : sig ... end

type t = private {

id : Base.string;
chr : Base.string;
strand : [ `Plus | `Minus ];
transcripts : Transcript.t Base.list;

}

val make : 
  id:Base.string ->
  strand:[ `Plus | `Minus ] ->
  (Base.string * GLoc.t Base.list) Base.list ->
  t Base.Or_error.t

val range : t -> Base.int * Base.int

val loc : t -> GLoc.t

val exons : t -> GLoc.t Base.list

val introns : t -> GLoc.t Base.list

val upstream : t -> Base.int -> GLoc.t

Warning: not right-clipped (unknown chromosome length)

val downstream : t -> Base.int -> GLoc.t

Warning: not right-clipped (unknown chromosome length)