package biotk

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package biotk
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Module BiotkSource

Sourcemodule Bai : sig ... end
Sourcemodule Bam_iterator : sig ... end
Sourcemodule Bed : sig ... end
Sourcemodule Cisbp : sig ... end
Sourcemodule Dataframe : sig ... end
Sourcemodule Dna_sequence : sig ... end
Sourcemodule Encode : sig ... end
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
Sourcemodule Gtf : sig ... end
Sourcemodule Idr : sig ... end

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

Sourcemodule Igv : sig ... end
Sourcemodule Interval_union : sig ... end
Sourcemodule Jaspar : sig ... end
Sourcemodule Let_syntax : sig ... end
Sourcemodule Line_oriented : sig ... end
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 Misc : sig ... end
Sourcemodule NarrowPeak : sig ... end
Sourcemodule Ncbi_genome : sig ... end
Sourcemodule Nucleotide : sig ... end
Sourcemodule Phylo_tree_draw : sig ... end
Sourcemodule Pipe_parsers : 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 Range : sig ... end
Sourcemodule Sam : sig ... end
Sourcemodule Ucsc_genome_browser : sig ... end
Sourcemodule Utils : sig ... end
Sourcemodule Wfa : sig ... end
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