package bistro-bio

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Paper: https://www.ncbi.nlm.nih.gov/pubmed/21700227 Datasets: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29506

val np : int
type chIP_sample = [
  1. | `ChIP_Pho4_noPi
  2. | `ChIP_Pho4_highPi
  3. | `ChIP_Cbf1_noPi
  4. | `ChIP_Mock_noPi
]
val pp_chIP_sample : Ppx_deriving_runtime.Format.formatter -> chIP_sample -> Ppx_deriving_runtime.unit
val show_chIP_sample : chIP_sample -> Ppx_deriving_runtime.string
val all_of_chIP_sample : chIP_sample list
type input_sample = [
  1. | `Input_Pho4_noPi
  2. | `Input_Pho4_highPi
  3. | `Input_Cbf1_noPi
  4. | `Input_Mock_noPi
]
val pp_input_sample : Ppx_deriving_runtime.Format.formatter -> input_sample -> Ppx_deriving_runtime.unit
val show_input_sample : input_sample -> Ppx_deriving_runtime.string
val all_of_input_sample : input_sample list
type sample = [
  1. | chIP_sample
  2. | input_sample
]
val pp_sample : Ppx_deriving_runtime.Format.formatter -> sample -> Ppx_deriving_runtime.unit
val show_sample : sample -> Ppx_deriving_runtime.string
val all_of_sample : sample list
type factor = [
  1. | `Pho4
  2. | `Cbf1
  3. | `Mock
]
val pp_factor : Ppx_deriving_runtime.Format.formatter -> factor -> Ppx_deriving_runtime.unit
val show_factor : factor -> Ppx_deriving_runtime.string
val all_of_factor : factor list
type condition = [
  1. | `noPi
  2. | `highPi
]
val pp_condition : Ppx_deriving_runtime.Format.formatter -> condition -> Ppx_deriving_runtime.unit
val show_condition : condition -> Ppx_deriving_runtime.string
val all_of_condition : condition list
val factor : [< `ChIP_Cbf1_highPi | `ChIP_Cbf1_noPi | `ChIP_Mock_highPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [> `Cbf1 | `Mock | `Pho4 ]
val condition : [< `ChIP_Cbf1_highPi | `ChIP_Cbf1_noPi | `ChIP_Mock_highPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [> `highPi | `noPi ]
val control_sample : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [> `Input_Cbf1_noPi | `Input_Mock_noPi | `Input_Pho4_highPi | `Input_Pho4_noPi ]
val srr_id : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi | `Input_Cbf1_noPi | `Input_Mock_noPi | `Input_Pho4_highPi | `Input_Pho4_noPi | `Input_WT_noPi ] -> string list
val fastq : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi | `Input_Cbf1_noPi | `Input_Mock_noPi | `Input_Pho4_highPi | `Input_Pho4_noPi | `Input_WT_noPi ] -> Bistro_bio.Fastq_sample.t Biotk.List1.t
val fastq_screen : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi | `Input_Cbf1_noPi | `Input_Mock_noPi | `Input_Pho4_highPi | `Input_Pho4_noPi | `Input_WT_noPi ] -> [ `fastq_screen ] Bistro.directory
val bowtie_index : [ `bowtie_index ] Bistro.directory
val mapped_reads : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi | `Input_Cbf1_noPi | `Input_Mock_noPi | `Input_Pho4_highPi | `Input_Pho4_noPi | `Input_WT_noPi ] -> Bistro_bio.Formats.sam Bistro.file
val mapped_reads_bam : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi | `Input_Cbf1_noPi | `Input_Mock_noPi | `Input_Pho4_highPi | `Input_Pho4_noPi | `Input_WT_noPi ] -> [ `indexed_bam ] Bistro.directory
val tf_peaks : ?qvalue:float -> [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [ `macs2_narrow ] Bistro.directory
val centered_tf_peaks : ?qvalue:float -> radius:int -> [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> Bistro_bio.Macs2.peak_summits Bistro.file
val best_macs_summits : ?qvalue:float -> n:int -> [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> 'a Bistro.path Bistro.workflow
val best_peak_sequences : ?nseqs:Core.Int.t -> ?qvalue:float -> radius:int -> [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> Bistro_bio.Formats.fasta Bistro.file
val meme : ?nseqs:Core.Int.t -> [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [ `meme ] Bistro.directory
val meme_motifs : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> 'a Bistro.path Bistro.workflow
val meme_chip : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [ `meme_chip ] Bistro.directory
val chipqc : [ `ChIPQC ] Bistro.directory
val occdist_vs_peak_score : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> Bistro.svg Bistro.file
val repo : Bistro_utils.Repo.item list
val run : unit -> unit
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