package biotk

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in-package search v0.2.0

package biotk

biotk
- Biotk
  - Alphabet
    
    Make
    
    _
    
    S
  - Amino_acid
  - Bai
  - Bam
    
    Alignment0
    
    Header
  - Bam_iterator
  - Bamstats
    
    Chr_histogram
    
    Fragment_length_histogram
  - 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
    
    _
  - Encode
    
    Experiment_list
  - Fasta
  - Fastq
    
    Stats
  - FeatureCounts
    
    Summary
    
    Tsv
    
    Fields
    
    Direct
  - GAnnot
    
    LAssoc
    
    LMap
    
    LSet
    
    Selection
  - GLoc
    
    Map
    
    Diff
    
    Key
    
    Provide_bin_io
    
    Key
    
    Provide_hash
    
    Key
    
    Provide_of_sexp
    
    Key
    
    Set
    
    Diff
    
    Elt
    
    Provide_bin_io
    
    Elt
    
    Provide_hash
    
    Elt
    
    Provide_of_sexp
    
    Elt
  - Gcf
  - Gene
    
    Transcript
  - Gff
    
    Annotation
    
    GFF2
    
    Item
    
    GFF3
    
    Item
    
    Record
    
    S
    
    Item
  - ISet
  - Ibed
  - 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
    
    _
    
    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
    
    Axis
    
    Colormap
    
    Font
    
    Plot
    
    Viewport
  - 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 Alphabet : sig ... end

Alphabet representation

module Amino_acid : sig ... end

An alphabet datatype representing amino-acids.

module Bai : sig ... end

BAI format: index for BAM file

module Bam : sig ... end

Read and write BAM format.

module Bam_iterator : sig ... end

Utility functions to traverse a BAM file

module Bamstats : sig ... end

module Bed : sig ... end

BED format

module Bgzf : sig ... end

I/O on Blocked GNU Zip format (BGZF) files

module Cisbp : sig ... end

Parsing of the Catalog of Inferred Sequence Binding Preferences

module Dataframe : sig ... end

Table parsing

module Dna_sequence : sig ... end

Deprecated. Utilities to handle DNA sequences

module Encode : sig ... end

Access to ENCODE data

module Fasta : sig ... end

module Fastq : sig ... end

module FeatureCounts : sig ... end

module GAnnot : sig ... end

Data structures to represent sets of (possibly annotated) genomic regions

module GLoc : sig ... end

module Gcf : sig ... end

GCF = Genomic coordinates format loosely defined as a TSV format whose first column represents a location with the syntax <chr>:<start>-<end>

module Gene : sig ... end

module Gff : sig ... end

General Feature Format

module ISet : sig ... end

DIET : Discrete Interval Encoding Trees

module Ibed : sig ... end

ibed format

module Idr : sig ... end

Utilities for the {https://github.com/nboley/idrIDR program

module Igv : sig ... end

module Interval_tree : sig ... end

Interval tree (data structure)

module Interval_union : sig ... end

module Jaspar : sig ... end

module Let_syntax : sig ... end

module Line : sig ... end

Single line of text.

module Line_oriented : sig ... end

Line-oriented file formats

module List1 : sig ... end

module Macs : sig ... end

https://github.com/taoliu/MACS/blob/macs_v1/README.rst

module Macs2 : sig ... end

Interaction with MACS2 peak caller

module Meme : sig ... end

module Misc : sig ... end

module NarrowPeak : sig ... end

module Ncbi_genome : sig ... end

module Nucleotide : sig ... end

module Phred_score : sig ... end

PHRED quality scores.

module Phylo_tree_draw : sig ... end

module Profile_matrix : sig ... end

module Pwm : sig ... end

Position-weight matrix

module Pwm_stats : sig ... end

Implementation of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238751/

module RanT : sig ... end

Range Traversal

module Range : sig ... end

Ranges of contiguous integers (integer intervals).

module Sam : sig ... end

SAM files. Documentation here assumes familiarity with the SAM specification.

module Solexa_score : sig ... end

Solexa quality scores.

module Ucsc_genome_browser : sig ... end

module Utils : sig ... end

module Wfa : sig ... end