bistro-bio 0.6.0 (latest) · OCaml Package

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 = [

| `ChIP_Pho4_noPi
| `ChIP_Pho4_highPi
| `ChIP_Cbf1_noPi
| `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 = [

| `Input_Pho4_noPi
| `Input_Pho4_highPi
| `Input_Cbf1_noPi
| `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 = [

| chIP_sample
| 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 = [

| `Pho4
| `Cbf1
| `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 = [

| `noPi
| `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 genome : Bistro_bio.Formats.fasta Bistro.file

val genome_2bit : Bistro_bio.Ucsc_gb.twobit Bistro.file

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 ecoli_genome : Bistro_bio.Formats.fasta Bistro.file

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 report : Bistro.html Bistro.file

val repo : Bistro_utils.Repo.item list

val run : unit -> unit

package bistro-bio