package biotk

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Module BiotkSource

Sourcemodule Alphabet : sig ... end

Alphabet representation

Sourcemodule Amino_acid : sig ... end

An alphabet datatype representing amino-acids.

Sourcemodule Bai : sig ... end

BAI format: index for BAM file

Sourcemodule Bam : sig ... end

Read and write BAM format.

Sourcemodule Bam_iterator : sig ... end

Utility functions to traverse a BAM file

Sourcemodule Bamstats : sig ... end
Sourcemodule Bed : sig ... end

BED format

Sourcemodule Bgzf : sig ... end

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

Sourcemodule Cisbp : sig ... end

Parsing of the Catalog of Inferred Sequence Binding Preferences

Sourcemodule Dataframe : sig ... end

Table parsing

Sourcemodule Dna_sequence : sig ... end

Deprecated. Utilities to handle DNA sequences

Sourcemodule Encode : sig ... end

Access to ENCODE data

Sourcemodule Fasta : sig ... end
Sourcemodule Fastq : sig ... end
Sourcemodule FeatureCounts : sig ... end
Sourcemodule GAnnot : sig ... end

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

Sourcemodule GLoc : sig ... end
Sourcemodule 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>

Sourcemodule Gene : sig ... end
Sourcemodule Gff : sig ... end

General Feature Format

Sourcemodule ISet : sig ... end

DIET : Discrete Interval Encoding Trees

Sourcemodule Ibed : sig ... end

ibed format

Sourcemodule Idr : sig ... end

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

Sourcemodule Igv : sig ... end
Sourcemodule Interval_tree : sig ... end

Interval tree (data structure)

Sourcemodule Interval_union : sig ... end
Sourcemodule Jaspar : sig ... end
Sourcemodule Let_syntax : sig ... end
Sourcemodule Line : sig ... end

Single line of text.

Sourcemodule Line_oriented : sig ... end

Line-oriented file formats

Sourcemodule List1 : sig ... end
Sourcemodule Macs : sig ... end

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

Sourcemodule Macs2 : sig ... end

Interaction with MACS2 peak caller

Sourcemodule Meme : sig ... end
Sourcemodule Misc : sig ... end
Sourcemodule NarrowPeak : sig ... end
Sourcemodule Ncbi_genome : sig ... end
Sourcemodule Nucleotide : sig ... end
Sourcemodule Phred_score : sig ... end

PHRED quality scores.

Sourcemodule Phylo_tree_draw : sig ... end
Sourcemodule Profile_matrix : sig ... end
Sourcemodule Pwm : sig ... end

Position-weight matrix

Sourcemodule Pwm_stats : sig ... end

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

Sourcemodule RanT : sig ... end

Range Traversal

Sourcemodule Range : sig ... end

Ranges of contiguous integers (integer intervals).

Sourcemodule Sam : sig ... end

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

Sourcemodule Solexa_score : sig ... end

Solexa quality scores.

Sourcemodule Ucsc_genome_browser : sig ... end
Sourcemodule Utils : sig ... end
Sourcemodule Wfa : sig ... end