package bistro

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package bistro

bistro
- Bistro
  - Private
  - Shell_dsl
  - Template_dsl
  - Workflow
  - binary_file
  - bz2
  - directory
  - file
  - gz
  - html
  - pdf
  - png
  - sexp_value
  - svg
  - tar
  - text_file
  - tsv
  - zip
bistro.bioinfo
- Bistro_bioinfo
  - Bed
  - Bedtools
    
    Cmd
  - Bowtie
    
    index
  - Bowtie2
    
    index
  - ChIPQC
    
    output
  - Cisa
  - DESeq2
    
    table
  - Deeptools
    
    compressed_numpy_array
    
    deeptools_matrix
  - Ensembl
  - FastQC
    
    report
  - Fastq
  - Fastq_screen
    
    output
  - Hisat2
  - Htseq
    
    count_tsv
  - Idba
  - Idr
  - Kallisto
    
    abundance_table
    
    index
  - Macs
    
    narrow_peaks
    
    output
    
    peak_summits
    
    peaks_xls
  - Macs2
    
    broad_output
    
    broad_peaks
    
    narrow_output
    
    narrow_peaks
    
    output
    
    peak_summits
    
    peaks_xls
  - Meme_suite
  - Picardtools
  - Prokka
  - Quast
  - Samtools
  - Spades
  - Sra_toolkit
  - Srst2
  - Star
  - Subread
    
    count_table
  - Tophat
    
    output
  - Ucsc_gb
    
    Lift_over
    
    chain_file
    
    output
    
    bedGraph
    
    bigBed
    
    bigWig
    
    chrom_sizes
    
    chromosome_sequences
    
    twobit
    
    wig
  - bam
  - bed3
  - bed4
  - bed5
  - bed6
  - fasta
  - fastq
  - gff
  - gff2
  - gff3
  - indexed_bam
  - phred64_fastq
  - sam
  - sanger_fastq
  - solexa_fastq
  - sra
bistro.engine
- Bistro_engine
  - Allocator
  - Db
  - Docker
  - Eval_thread
    
    Infix
  - Execution_env
  - Execution_trace
  - Local_backend
  - Logger
    
    t
  - Lwt_queue
  - Misc
  - Path
  - Scheduler
    
    Backend
    
    Gc
    
    Make
    
    Backend
  - Shell_command
  - Singularity
  - Task_result
bistro.internals
- Bistro_internals
  - Command
    
    Docker_image
    
    Singularity_image
  - Template
  - Workflow
    
    Any
    
    Map
    
    Set
    
    Table
bistro.multinode
- Bistro_multinode
  - Client
  - Server
bistro.nlp
- Bistro_nlp
  - Stanford_parser
    
    deps
bistro.unix
- Bistro_unix
  - Cmd
bistro.utils
- Bistro_utils

Legend:
Library
Module
Module type
Parameter
Class
Class type

type 'a signal_format

val bigwig : Ucsc_gb.bigWig signal_format

val bedgraph : Ucsc_gb.bedGraph signal_format

type 'a img_format

val png : Bistro.png img_format

val pdf : Bistro.pdf img_format

val svg : Bistro.svg img_format

val bamcoverage : 
  ?scalefactor:float ->
  ?filterrnastrand:[ `forward | `reverse ] ->
  ?binsize:int ->
  ?blacklist:bed3 Bistro.pworkflow ->
  ?threads:int ->
  ?normalizeUsing:[ `RPKM | `CPM | `BPM | `RPGC ] ->
  ?ignorefornormalization:string list ->
  ?skipnoncoveredregions:bool ->
  ?smoothlength:int ->
  ?extendreads:int ->
  ?ignoreduplicates:bool ->
  ?minmappingquality:int ->
  ?centerreads:bool ->
  ?samflaginclude:int ->
  ?samflagexclude:int ->
  ?minfragmentlength:int ->
  ?maxfragmentlength:int ->
  'a signal_format ->
  indexed_bam Bistro.pworkflow ->
  'a Bistro.pworkflow

val bamcompare : 
  ?scalefactormethod:[ `readcount | `ses ] ->
  ?samplelength:int ->
  ?numberofsamples:int ->
  ?scalefactor:float ->
  ?ratio:
    [ `log2
    | `ratio
    | `subtract
    | `add
    | `mean
    | `reciprocal_ratio
    | `first
    | `second ] ->
  ?pseudocount:int ->
  ?binsize:int ->
  ?region:string ->
  ?blacklist:bed3 Bistro.pworkflow ->
  ?threads:int ->
  ?normalizeUsing:[ `RPKM | `CPM | `BPM | `RPGC ] ->
  ?ignorefornormalization:string list ->
  ?skipnoncoveredregions:bool ->
  ?smoothlength:int ->
  ?extendreads:int ->
  ?ignoreduplicates:bool ->
  ?minmappingquality:int ->
  ?centerreads:bool ->
  ?samflaginclude:int ->
  ?samflagexclude:int ->
  ?minfragmentlength:int ->
  ?maxfragmentlength:int ->
  'a signal_format ->
  indexed_bam Bistro.pworkflow ->
  indexed_bam Bistro.pworkflow ->
  'a Bistro.pworkflow

val bigwigcompare : 
  ?scalefactor:float ->
  ?ratio:
    [ `log2
    | `ratio
    | `subtract
    | `add
    | `mean
    | `reciprocal_ratio
    | `first
    | `second ] ->
  ?pseudocount:int ->
  ?binsize:int ->
  ?region:string ->
  ?blacklist:bed3 Bistro.pworkflow ->
  ?threads:int ->
  'a signal_format ->
  Ucsc_gb.bigWig Bistro.pworkflow ->
  Ucsc_gb.bigWig Bistro.pworkflow ->
  'a Bistro.pworkflow

class type compressed_numpy_array = object ... end

val multibamsummary_bins : 
  ?binsize:int ->
  ?distancebetweenbins:int ->
  ?region:string ->
  ?blacklist:bed3 Bistro.pworkflow ->
  ?threads:int ->
  ?outrawcounts:bool ->
  ?extendreads:int ->
  ?ignoreduplicates:bool ->
  ?minmappingquality:int ->
  ?centerreads:bool ->
  ?samflaginclude:int ->
  ?samflagexclude:int ->
  ?minfragmentlength:int ->
  ?maxfragmentlength:int ->
  indexed_bam Bistro.pworkflow list ->
  compressed_numpy_array Bistro.pworkflow

val multibamsummary_bed : 
  ?region:string ->
  ?blacklist:bed3 Bistro.pworkflow ->
  ?threads:int ->
  ?outrawcounts:bool ->
  ?extendreads:int ->
  ?ignoreduplicates:bool ->
  ?minmappingquality:int ->
  ?centerreads:bool ->
  ?samflaginclude:int ->
  ?samflagexclude:int ->
  ?minfragmentlength:int ->
  ?maxfragmentlength:int ->
  ?metagene:bool ->
  ?transcriptid:bool ->
  ?exonid:bool ->
  ?transcriptiddesignator:bool ->
  bed3 Bistro.pworkflow ->
  indexed_bam Bistro.pworkflow list ->
  compressed_numpy_array Bistro.pworkflow

class type deeptools_matrix = object ... end

val computeMatrix_reference_point : 
  ?referencePoint:[ `TSS | `TES | `center ] ->
  ?upstream:int ->
  ?downstream:int ->
  ?nanAfterEnd:bool ->
  ?binSize:int ->
  ?sortRegions:[ `descend | `ascend | `no | `keep ] ->
  ?sortUsing:[ `mean | `median | `max | `min | `sum | `region_length ] ->
  ?sortUsingSamples:int list ->
  ?averageTypeBins:[ `mean | `median | `min | `max | `std | `sum ] ->
  ?missingDataAsZero:bool ->
  ?skipZeros:bool ->
  ?minThreshold:float ->
  ?maxThreshold:float ->
  ?blackList:bed3 Bistro.pworkflow ->
  ?scale:float ->
  ?numberOfProcessors:int ->
  regions:bed3 Bistro.pworkflow list ->
  scores:Ucsc_gb.bigWig Bistro.pworkflow list ->
  unit ->
  deeptools_matrix Bistro.gz Bistro.pworkflow

val plotHeatmap : 
  ?dpi:int ->
  ?kmeans:int ->
  ?hclust:int ->
  ?sortRegions:[ `descend | `ascend | `no ] ->
  ?sortUsing:[ `mean | `median | `max | `min | `sum | `region_length ] ->
  ?sortUsingSamples:int list ->
  ?averageTypeSummaryPlot:[ `mean | `median | `min | `max | `std | `sum ] ->
  ?missingDataColor:string ->
  ?colorMap:string ->
  ?alpha:float ->
  ?colorList:string list ->
  ?colorNumber:int ->
  ?zMin:float list ->
  ?zMax:float list ->
  ?heatmapHeight:float ->
  ?heatmapWidth:float ->
  ?whatToShow:
    [ `plot_heatmap_and_colorbar
    | `plot_and_heatmap
    | `heatmap_only
    | `heatmap_and_colorbar ] ->
  ?boxAroundHeatmaps:bool ->
  ?xAxisLabel:string ->
  ?startLabel:string ->
  ?endLabel:string ->
  ?refPointLabel:string ->
  ?regionsLabel:string list ->
  ?samplesLabel:string list ->
  ?plotTitle:string ->
  ?yAxisLabel:string ->
  ?yMin:float list ->
  ?yMax:float list ->
  ?legendLocation:
    [ `best
    | `upper_right
    | `upper_left
    | `upper_center
    | `lower_left
    | `lower_right
    | `lower_center
    | `center
    | `center_left
    | `center_right
    | `none ] ->
  ?perGroup:bool ->
  'a img_format ->
  deeptools_matrix Bistro.gz Bistro.pworkflow ->
  'a Bistro.pworkflow

val plotCorrelation : 
  ?skipZeros:bool ->
  ?labels:string list ->
  ?plotTitle:string ->
  ?removeOutliers:bool ->
  ?colorMap:string ->
  ?plotNumbers:bool ->
  ?log1p:bool ->
  corMethod:[ `spearman | `pearson ] ->
  whatToPlot:[ `heatmap | `scatterplot ] ->
  'a img_format ->
  compressed_numpy_array Bistro.pworkflow ->
  'a Bistro.pworkflow

val plotProfile : 
  ?dpi:int ->
  ?kmeans:int ->
  ?hclust:int ->
  ?averageType:[ `mean | `median | `min | `max | `std | `sum ] ->
  ?plotHeight:float ->
  ?plotWidth:float ->
  ?plotType:[ `lines | `fill | `se | `std | `overlapped_lines | `heatmap ] ->
  ?colors:string list ->
  ?numPlotsPerRow:int ->
  ?startLabel:string ->
  ?endLabel:string ->
  ?refPointLabel:string ->
  ?regionsLabel:string list ->
  ?samplesLabel:string list ->
  ?plotTitle:string ->
  ?yAxisLabel:string ->
  ?yMin:float list ->
  ?yMax:float list ->
  ?legendLocation:
    [ `best
    | `upper_right
    | `upper_left
    | `upper_center
    | `lower_left
    | `lower_right
    | `lower_center
    | `center
    | `center_left
    | `center_right
    | `none ] ->
  ?perGroup:bool ->
  'a img_format ->
  deeptools_matrix Bistro.gz Bistro.pworkflow ->
  'a Bistro.pworkflow

val plotEnrichment : 
  ?labels:string list ->
  ?regionLabels:string list ->
  ?plotTitle:string ->
  ?variableScales:bool ->
  ?plotHeight:float ->
  ?plotWidth:float ->
  ?colors:string list ->
  ?numPlotsPerRow:int ->
  ?alpha:float ->
  ?offset:int ->
  ?blackList:bed3 Bistro.pworkflow ->
  ?numberOfProcessors:int ->
  bams:bam Bistro.pworkflow list ->
  beds:bed3 Bistro.pworkflow list ->
  'a img_format ->
  'a Bistro.pworkflow