biotk 0.1.0

Libraries

This package provides the following libraries (via dune):

biotk

Documentation:

• Biotk.Bai
• Biotk.Bam_iterator
• Biotk.Bed
• Biotk.Cisbp
• Biotk.Dataframe
• Biotk.Dna_sequence
• Biotk.Encode
• Biotk.Fasta
• Biotk.Fastq
• Biotk.FeatureCounts
• Biotk.GAnnot Data structures to represent sets of (possibly annotated) genomic regions
• Biotk.GLoc
• Biotk.Gcf GCF = Genomic coordinates format loosely defined as a TSV format whose first column represents a location with the syntax <chr>:<start>-<end>
• Biotk.Gene
• Biotk.Gff
• Biotk.Gtf
• Biotk.Idr Utilities for the {https://github.com/nboley/idrIDR program
• Biotk.Igv
• Biotk.Interval_union
• Biotk.Jaspar
• Biotk.Let_syntax
• Biotk.Line_oriented
• Biotk.List1
• Biotk.Macs https://github.com/taoliu/MACS/blob/macs_v1/README.rst
• Biotk.Macs2 Interaction with MACS2 peak caller
• Biotk.Misc
• Biotk.NarrowPeak
• Biotk.Ncbi_genome
• Biotk.Nucleotide
• Biotk.Phylo_tree_draw
• Biotk.Pipe_parsers
• Biotk.Profile_matrix
• Biotk.Pwm Position-weight matrix
• Biotk.Pwm_stats Implementation of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238751/
• Biotk.RanT Range Traversal
• Biotk.Range
• Biotk.Sam
• Biotk.Ucsc_genome_browser
• Biotk.Utils
• Biotk.Wfa

Dependencies: angstrom.unix, biocaml.unix, biotk.croquis, biotk.pipes.unix, cfstream, core_kernel, fmt, tyxml, ppx_sexp_conv.runtime-lib, ppx_inline_test.runtime-lib, fieldslib, ppx_here.runtime-lib, ppx_expect.collector, ppx_expect.config, ppx_deriving.runtime, csvfields, ppx_compare.runtime-lib

biotk.croquis

Documentation:

• Biotk_croquis.Croquis
• Biotk_croquis.Font_data
• Biotk_croquis.Vg_text

Dependencies: core_kernel, otfm, vg, vg.pdf, vg.svg

biotk.pipes

Documentation:

• Biotk_pipes.Pipe

biotk.pipes.unix

Documentation:

• Biotk_pipes_unix.Pipe

Dependencies: biotk.pipes