package biotk

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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
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