package bistro-bio

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package bistro-bio
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Module Bistro_bio_examples.Zhou2011Source

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

Sourceval np : int
Sourcetype chIP_sample = [
  1. | `ChIP_Pho4_noPi
  2. | `ChIP_Pho4_highPi
  3. | `ChIP_Cbf1_noPi
  4. | `ChIP_Mock_noPi
]
Sourceval all_of_chIP_sample : chIP_sample list
Sourcetype input_sample = [
  1. | `Input_Pho4_noPi
  2. | `Input_Pho4_highPi
  3. | `Input_Cbf1_noPi
  4. | `Input_Mock_noPi
]
Sourceval all_of_input_sample : input_sample list
Sourcetype sample = [
  1. | chIP_sample
  2. | input_sample
]
Sourceval all_of_sample : sample list
Sourcetype factor = [
  1. | `Pho4
  2. | `Cbf1
  3. | `Mock
]
Sourceval all_of_factor : factor list
Sourcetype condition = [
  1. | `noPi
  2. | `highPi
]
Sourceval all_of_condition : condition list
Sourceval factor : [< `ChIP_Cbf1_highPi | `ChIP_Cbf1_noPi | `ChIP_Mock_highPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [> `Cbf1 | `Mock | `Pho4 ]
Sourceval condition : [< `ChIP_Cbf1_highPi | `ChIP_Cbf1_noPi | `ChIP_Mock_highPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [> `highPi | `noPi ]
Sourceval 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 ]
Sourceval genome : Bistro_bio.Formats.fasta Bistro.file
Sourceval genome_2bit : Bistro_bio.Ucsc_gb.twobit Bistro.file
Sourceval 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
Sourceval 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
Sourceval ecoli_genome : Bistro_bio.Formats.fasta Bistro.file
Sourceval 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
Sourceval bowtie_index : [ `bowtie_index ] Bistro.directory
Sourceval 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
Sourceval 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
Sourceval tf_peaks : ?qvalue:float -> [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [ `macs2_narrow ] Bistro.directory
Sourceval 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
Sourceval best_macs_summits : ?qvalue:float -> n:int -> [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> 'a Bistro.path Bistro.workflow
Sourceval 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
Sourceval meme : ?nseqs:Core.Int.t -> [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [ `meme ] Bistro.directory
Sourceval meme_motifs : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> 'a Bistro.path Bistro.workflow
Sourceval meme_chip : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> [ `meme_chip ] Bistro.directory
Sourceval chipqc : [ `ChIPQC ] Bistro.directory
Sourceval occdist_vs_peak_score : [< `ChIP_Cbf1_noPi | `ChIP_Mock_noPi | `ChIP_Pho4_highPi | `ChIP_Pho4_noPi ] -> Bistro.svg Bistro.file
Sourceval report : Bistro.html Bistro.file
Sourceval run : unit -> unit
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